Created new feature branch for PR as per request
This commit is contained in:
Oliver Henrich
@ -72,7 +72,7 @@ between two individual nucleotides can be established.
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/******************************************************************************/
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/examples/oxRNA2/duplex4
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/examples/oxRNA2/duplex2
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This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or
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oxDNA2 force field. Sequence-dependent stacking and hydrogen-bonding
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@ -1,15 +1,14 @@
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# LAMMPS data file
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LAMMPS data file via write_data, version 27 May 2021
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10 atoms
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10 ellipsoids
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8 bonds
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4 atom types
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8 bonds
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1 bond types
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10 ellipsoids
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# System size
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-20.000000 20.000000 xlo xhi
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-20.000000 20.000000 ylo yhi
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-20.000000 20.000000 zlo zhi
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-20 20 xlo xhi
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-20 20 ylo yhi
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-20 20 zlo zhi
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Masses
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@ -18,56 +17,52 @@ Masses
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3 3.1575
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4 3.1575
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# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
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Atoms
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Atoms # hybrid
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1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
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2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
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3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
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4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
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5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
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6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
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7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
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8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
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9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
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10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
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1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0
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2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0
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3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0
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4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0
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5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0
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6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0
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7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0
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8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0
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9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0
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10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0
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# Atom-ID, translational velocity, angular momentum
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Velocities
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1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397
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2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385
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3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783
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4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775
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5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883
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6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354
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7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567
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8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627
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9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048
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10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025
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# Atom-ID, shape, quaternion
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Ellipsoids
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1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
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3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
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4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
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5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
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6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
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7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
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8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
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9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
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10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
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# Bond topology
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Bonds
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1 1 1 2
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2 1 2 3
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3 1 3 4
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4 1 4 5
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5 1 6 7
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6 1 7 8
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7 1 8 9
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8 1 9 10
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1 1 1 2
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2 1 2 3
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3 1 3 4
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4 1 4 5
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5 1 6 7
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6 1 7 8
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7 1 8 9
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8 1 9 10
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Ellipsoids
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1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
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2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
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3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
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4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
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5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
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6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
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7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
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8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
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9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
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10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
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@ -11,11 +11,11 @@ newton off
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boundary p p p
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atom_style hybrid bond ellipsoid
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atom_style hybrid bond ellipsoid oxdna
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atom_modify sort 0 1.0
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# Pair interactions require lists of neighbours to be calculated
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neighbor 1.0 bin
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neighbor 2.0 bin
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neigh_modify every 1 delay 0 check yes
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read_data data.duplex1
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@ -40,27 +40,16 @@ pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793
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pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
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# NVE ensemble
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fix 1 all nve/dot
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#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
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#fix 1 all nve/asphere
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#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
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fix 1 all nve/asphere
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#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
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||||
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timestep 1e-5
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#comm_style tiled
|
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#fix 3 all balance 10000 1.1 rcb
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comm_modify cutoff 2.5
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fix 3 all balance 1000 1.03 shift xyz 10 1.03
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comm_modify cutoff 3.8
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
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|
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#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
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#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
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#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -71,10 +60,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
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||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,15 +1,14 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
16 atoms
|
||||
16 ellipsoids
|
||||
13 bonds
|
||||
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
@ -18,79 +17,75 @@ Masses
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
|
||||
7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
|
||||
10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
|
||||
11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
|
||||
12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
|
||||
13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
|
||||
14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0
|
||||
14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0
|
||||
15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0
|
||||
16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725
|
||||
2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215
|
||||
3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625
|
||||
4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877
|
||||
5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292
|
||||
6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776
|
||||
7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357
|
||||
8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032
|
||||
9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696
|
||||
10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506
|
||||
11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418
|
||||
12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697
|
||||
13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132
|
||||
14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759
|
||||
15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106
|
||||
16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
|
||||
@ -11,11 +11,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
@ -40,27 +40,16 @@ pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -71,10 +60,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,15 +1,14 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
10 atoms
|
||||
10 ellipsoids
|
||||
8 bonds
|
||||
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
@ -18,56 +17,52 @@ Masses
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
|
||||
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
|
||||
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0
|
||||
6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0
|
||||
7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0
|
||||
8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0
|
||||
9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0
|
||||
10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397
|
||||
2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385
|
||||
3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783
|
||||
4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775
|
||||
5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883
|
||||
6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354
|
||||
7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567
|
||||
8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627
|
||||
9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048
|
||||
10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
|
||||
@ -2,6 +2,7 @@ variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -11,11 +12,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -72,10 +62,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,15 +1,14 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
16 atoms
|
||||
16 ellipsoids
|
||||
13 bonds
|
||||
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
@ -18,79 +17,75 @@ Masses
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
|
||||
7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
|
||||
10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
|
||||
11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
|
||||
12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
|
||||
13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
|
||||
14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0
|
||||
14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0
|
||||
15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0
|
||||
16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725
|
||||
2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215
|
||||
3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625
|
||||
4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877
|
||||
5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292
|
||||
6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776
|
||||
7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357
|
||||
8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032
|
||||
9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696
|
||||
10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506
|
||||
11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418
|
||||
12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697
|
||||
13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132
|
||||
14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759
|
||||
15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106
|
||||
16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
|
||||
@ -2,6 +2,7 @@ variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -11,11 +12,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -72,10 +62,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,73 +1,68 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
10 atoms
|
||||
10 ellipsoids
|
||||
8 bonds
|
||||
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
2 1.0
|
||||
3 1.0
|
||||
4 1.0
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
|
||||
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
|
||||
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
1 1 -0.11270997503399371 -0.7862611620723637 1.3165400870544903 1 1 0.060395054525384434 0 0 0
|
||||
2 2 -0.16100240482903602 -1.0148422652606093 1.7725173088171975 1 1 0.060395054525384434 0 0 0
|
||||
3 3 -0.07298109176865208 -1.2058352049378398 2.2155374630046025 1 1 0.060395054525384434 0 0 0
|
||||
4 4 0.20885923193243378 -1.2688318677749852 2.7293157091426354 1 1 0.060395054525384434 0 0 0
|
||||
5 1 0.4977080746488808 -1.1877183116613397 3.1217952838980874 1 1 0.060395054525384434 0 0 0
|
||||
6 4 -0.2268968274787041 -0.189603020612256 3.1084583050105072 2 1 0.060395054525384434 0 0 0
|
||||
7 1 -0.0350302960648884 -0.11245734514413211 2.7014501755341493 2 1 0.060395054525384434 0 0 0
|
||||
8 2 0.25244681036675387 -0.03694235704351071 2.3220950502861553 2 1 0.060395054525384434 0 0 0
|
||||
9 3 0.6676541258850296 -0.19471246409842435 2.0340464261767104 2 1 0.060395054525384434 0 0 0
|
||||
10 4 0.934602266948905 -0.5194117909409754 1.8612193115349325 2 1 0.060395054525384434 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.7350861197179651 -0.21340767305489933 0.039697389523131524 0.514970941606362 -0.5778402699166201 0.41643574848945447
|
||||
2 0.45886825731636693 0.15479323180826426 0.45998155912439004 -0.09532046111956156 -0.028811462065931184 0.1672428695820793
|
||||
3 -0.10009582230026307 -0.1356043155573722 -0.1357102030132947 0.512435093836635 0.8794667047362844 -0.4062045597142004
|
||||
4 -0.030407148345627223 -0.009119685021467273 0.2894674569635424 -0.22197357320787495 0.46474035192627294 -0.07166539037437039
|
||||
5 0.021807141873185235 -0.3544326055489752 0.4440408124043861 -0.019877710182688496 0.008454084203717545 -0.16574323908949498
|
||||
6 0.058814594979770644 -0.23964725458291067 0.09430081861001074 -0.16841516333125345 -0.27499692207835863 0.49231682345951117
|
||||
7 -0.004278840261670186 0.011171100752661912 -0.10686407869958243 0.3533956051874728 -0.5781793964284943 0.171273466705473
|
||||
8 -0.5678723978567293 -0.05635280062816237 -0.12337612014269532 -0.06293014166900977 -0.5548255617488771 -0.3948679676680598
|
||||
9 0.07493146865794496 0.37868089841113717 0.11143666048372917 -0.35561925325917687 -0.3453461570214745 -0.5277976799082732
|
||||
10 -0.48819053761319386 -0.11027061946453155 0.19465531836187655 0.10340969323917759 0.3809806548307742 0.25623918588602335
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
|
||||
7 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
|
||||
8 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
9 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
|
||||
10 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.9824438652148015 -0.023183015026523597 -0.18238525095550406 0.031657854475291056
|
||||
2 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.9303156820429525 0.02962373336578937 -0.07607439157272995 0.3575581814380256
|
||||
3 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.7912072782182723 -0.043679545103099016 -0.05996218100443608 0.6070318583758278
|
||||
4 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.6531869542452552 -0.03659000162837596 0.004181596561545229 0.7563005281201641
|
||||
5 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.3249781771672557 0.06207197535108856 0.03689277251937633 0.9429608568635791
|
||||
6 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.08029535222204207 0.8726095530830543 -0.46831094470633033 -0.11309325067392484
|
||||
7 3.1622776601683795 3.1622776601683795 3.1622776601683795 -0.1303991484205687 0.7764383491760718 -0.6081660772848121 0.10135864274905797
|
||||
8 3.1622776601683795 3.1622776601683795 3.1622776601683795 -0.14971034142173664 0.5769499085020084 -0.7973230447846137 0.09482393688465168
|
||||
9 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.21130729744233523 -0.37917864508185584 0.8946270178621702 -0.10590221939385809
|
||||
10 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.34278400171414436 0.15185237372800306 0.9252984668160771 0.05712032974191834
|
||||
|
||||
@ -2,6 +2,7 @@ variable number equal 3
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -11,11 +12,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex3
|
||||
@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -72,10 +62,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,130 +1,132 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
26 atoms
|
||||
26 ellipsoids
|
||||
24 bonds
|
||||
|
||||
4 atom types
|
||||
24 bonds
|
||||
1 bond types
|
||||
26 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Masses
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1
|
||||
7 3 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1
|
||||
10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1
|
||||
11 3 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1
|
||||
12 4 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1
|
||||
13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1
|
||||
14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1
|
||||
15 1 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1
|
||||
16 2 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1
|
||||
17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1
|
||||
18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1
|
||||
19 1 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1
|
||||
20 2 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1
|
||||
21 3 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1
|
||||
22 4 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1
|
||||
23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1
|
||||
24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1
|
||||
25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1
|
||||
26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.5974293795290144 -0.47217734566783476 0.1149860099192362 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.3607975285447209 -0.8084200276362509 0.5005631273908187 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.1880165420620915 -0.9339012982528754 0.9372222930006777 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.18789028377909187 -0.8807473585891459 1.3080750447260532 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.46680288593900887 -0.6314504249974493 1.6544618495816525 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.6156490001978658 -0.24344915610488765 1.9998398114466447 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.5475869309223161 0.10633006738807783 2.395688109397028 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.3964561058464781 0.33864915662119616 2.855380256681012 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.09151778690925949 0.33572177117709545 3.2793107140407853 1 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.260700239272384 0.23452584272483473 3.622064753017485 1 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.44049173083867876 -0.04240311520575983 4.057361772274168 1 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.48111471327910416 -0.3913669550617015 4.465217350523367 1 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.3029890593292223 -0.6218232516387349 4.889919411438907 1 1 3.7269849963023267 0 0 0
|
||||
14 4 0.36538593166250877 0.467104033114044 4.885957202043727 2 1 3.7269849963023267 0 0 0
|
||||
15 1 0.5837256243756591 0.1432569770282543 4.587937684834979 2 1 3.7269849963023267 0 0 0
|
||||
16 2 0.7270895848434721 -0.21648156960230241 4.19127441749994 2 1 3.7269849963023267 0 0 0
|
||||
17 3 0.5694364623788377 -0.5971020505771416 3.7905394408535833 2 1 3.7269849963023267 0 0 0
|
||||
18 4 0.32183479629572403 -0.7826674384502239 3.3981789941001397 2 1 3.7269849963023267 0 0 0
|
||||
19 1 0.027943077828669855 -0.8173952163019756 2.892497591992246 2 1 3.7269849963023267 0 0 0
|
||||
20 2 -0.34389471043742403 -0.6801076538339801 2.6010059142333977 2 1 3.7269849963023267 0 0 0
|
||||
21 3 -0.5722337592890715 -0.31543771192866543 2.2496367888009035 2 1 3.7269849963023267 0 0 0
|
||||
22 4 -0.5243059431454682 -0.018794840926191582 1.6669602274961965 2 1 3.7269849963023267 0 0 0
|
||||
23 1 -0.4467049661654279 0.15318137385858244 1.1669311078565738 2 1 3.7269849963023267 0 0 0
|
||||
24 2 -0.04279541944801792 0.24071675674438053 0.7924196804793574 2 1 3.7269849963023267 0 0 0
|
||||
25 3 0.33688934798342335 0.1390449738629785 0.42004977704361546 2 1 3.7269849963023267 0 0 0
|
||||
26 4 0.5381606093378432 -0.28366941895261566 0.04905784853961178 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 -0.1420563695014878 -0.2339928257547227 0.1871716305399088 -0.046333854442252194 0.08160574816172744 0.2791824603833533
|
||||
2 0.03390382747481304 0.2912921705525512 -0.1828986721885175 0.09422531767061365 -0.044398236946770545 0.011069519340877812
|
||||
3 0.05351747745964457 -0.3700026678535097 -0.01469442373794632 0.10875858697088675 0.2373869034785703 0.15028498953263314
|
||||
4 0.1107696836820372 0.012571134739153464 0.23554381030898286 0.11411649786729211 -0.23899527406990237 0.11196343804383825
|
||||
5 0.21949033826324368 -0.4153000294565104 0.18426481814713022 0.2497206165366295 0.2505624077277829 -0.35347918243093
|
||||
6 -0.24019769428878804 -0.16423570219236758 -0.003762466815720382 0.062008045889015595 0.22340307597010978 -0.38223196779931135
|
||||
7 0.12372477399377596 0.10393016373901434 0.08008946447311854 -0.15063203100274558 0.08544129561789665 -0.3233996805084572
|
||||
8 0.03216353270652909 -0.1291938805451393 0.1736283537356162 -0.17577447248216746 0.11132849782859955 -0.13659117762014125
|
||||
9 0.016485625003622013 0.01204732455105311 0.012268845318149781 -0.10829791072979295 0.1325154323216732 0.061321711941405295
|
||||
10 -0.10017034720683878 -0.09274368063499111 0.0712704971413183 -0.08539556363371427 -0.10194584018083674 0.12395163271335013
|
||||
11 0.1553620769751766 -0.017877616757193807 -0.1679552227127468 -0.11302061465460307 0.10833285249943261 -0.29004856929349787
|
||||
12 -0.25308607960176693 0.05651778438229357 -0.28293751231512154 0.08875447438401544 -0.0424858854741496 0.4807657704475166
|
||||
13 -0.006525152792083277 0.05278468067247092 0.0923614993309851 -0.17068957621149589 -0.21396827821680875 -0.22336174340467796
|
||||
14 -0.09024428084565417 0.19407821508904713 -0.27279958154128003 0.16579397498898726 0.05605196163049078 0.18139063086724955
|
||||
15 0.2329539015603435 0.08926675461196792 0.01755751945261716 0.14895763843533014 0.05566424996653055 0.038429304115211504
|
||||
16 -0.012766107314323394 -0.05870276075293287 0.22459362070331024 -0.051898555487544795 0.11349183901118838 -0.35625338947479507
|
||||
17 -0.20400754456760709 -0.43178141581578006 -0.05213026263746946 -0.16561150375144387 -0.08257869123336893 -0.31368221607714253
|
||||
18 0.26408469209202234 0.004101215813165573 -0.11409222616552296 -0.37751548716793587 0.021230702354981583 0.23218952685038605
|
||||
19 -0.2811352347889802 0.25474603468997514 0.0038005485218010606 0.2164466860189806 -0.3924452117278991 0.22754829879548555
|
||||
20 -0.34129793271588454 0.05074672818229578 -0.03388446943745919 -0.1368254010552013 -0.1547809974693013 -0.03266259795645136
|
||||
21 -0.25700758391191114 0.04693154859703793 0.08362546455733241 -0.08661574368141227 -0.030723569920460755 -0.18740437515161282
|
||||
22 0.08529314327765061 0.10662056255177826 -0.0742729015142829 -0.4671828719407557 -0.19246067344838313 0.20137866804242557
|
||||
23 -0.09337250162399305 -0.1907111010034805 0.19278254253312255 0.017795209772695803 -0.36506106427644847 0.24972052729172167
|
||||
24 -0.16063305395742022 0.12278800901705311 0.0513923554335936 -0.09716260028970423 -0.26401680055506943 0.08202659665577536
|
||||
25 -0.14736287972598905 0.09699085150412592 -0.20751532907712478 0.05612191742480806 -0.13929212905625324 0.034890079586931765
|
||||
26 -0.060417626533246734 0.35551862988152244 -0.19673503245092067 0.014766691426271806 0.02762183997756995 -0.20597323908506235
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00
|
||||
17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00
|
||||
18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00
|
||||
19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00
|
||||
20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00
|
||||
21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00
|
||||
22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00
|
||||
23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00
|
||||
24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00
|
||||
25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00
|
||||
26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9970278940278272 0.0014876174054512252 0.0750547523448584 0.017319055267040844
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9059171712388804 0.007913225291438054 0.04634256838354512 0.42083705406683053
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.7657426991864452 0.028071560533125216 0.13224385975981257 0.6287779160305484
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5238981696613685 0.0516703526741727 0.1609645534282743 0.8348360887142046
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.30973290897949424 0.0750672191209306 0.23962885621884192 0.9170651279902646
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.050269263744563454 0.08142241031464711 0.09584085715741358 0.9907865170259763
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.3805122714271814 0.08965734720629535 0.057827749665601925 0.9186010683391725
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.6066322463100545 0.015286960797006149 0.035984536832974555 0.7940206166563465
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.771660293819677 0.02607541526374929 -0.08047223278265907 -0.6303845520092687
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.9119628434851113 0.03686258000931541 -0.11017000132786052 -0.3934812487336936
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 0.9917294290821066 0.05835078551401739 -0.08073737536574405 -0.08092837290732445
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 0.9763527785523285 0.06753089597617556 0.004847281702108697 0.205307899901351
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 0.8553397145502984 0.1399133966151149 0.07233200118835512 0.49354462388392356
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.014416326682630282 -0.533642571147991 0.8442695396252617 0.04718813669228716
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 0.14095892784917538 -0.2201285495070387 0.9406003462562982 -0.21666792788520955
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 0.07323967796304806 0.05035907488974361 0.963136526452943 -0.2539053850556888
|
||||
17 1.173984503142341 1.173984503142341 1.173984503142341 0.030254986187638885 0.39195467212588947 0.9164794947567249 -0.07430684019611289
|
||||
18 1.173984503142341 1.173984503142341 1.173984503142341 -0.03080283760241768 0.6526511470205414 0.7481495879677094 -0.11562810865943304
|
||||
19 1.173984503142341 1.173984503142341 1.173984503142341 -0.09450197979153381 0.7469150592813072 0.6556128255138505 -0.0579576833217777
|
||||
20 1.173984503142341 1.173984503142341 1.173984503142341 -0.12903334341475137 0.9222523214328698 0.3501336268694509 -0.10103214950765672
|
||||
21 1.173984503142341 1.173984503142341 1.173984503142341 -0.0069954457806870336 0.9888131084284681 -0.09413955816471489 -0.11548785185859346
|
||||
22 1.173984503142341 1.173984503142341 1.173984503142341 0.029336230851923526 0.9805894852440379 -0.19236800606724952 -0.02404573205262194
|
||||
23 1.173984503142341 1.173984503142341 1.173984503142341 0.03080980270092377 0.872234086776475 -0.4869211139732921 0.03415088124407873
|
||||
24 1.173984503142341 1.173984503142341 1.173984503142341 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672
|
||||
25 1.173984503142341 1.173984503142341 1.173984503142341 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346
|
||||
26 1.173984503142341 1.173984503142341 1.173984503142341 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467
|
||||
|
||||
@ -1,130 +1,136 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
26 atoms
|
||||
26 ellipsoids
|
||||
24 bonds
|
||||
|
||||
8 atom types
|
||||
24 bonds
|
||||
1 bond types
|
||||
26 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Masses
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1
|
||||
5 5 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1
|
||||
6 6 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1
|
||||
7 7 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1
|
||||
8 8 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1
|
||||
10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1
|
||||
11 7 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1
|
||||
12 8 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1
|
||||
13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1
|
||||
14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1
|
||||
15 5 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1
|
||||
16 6 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1
|
||||
17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1
|
||||
18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1
|
||||
19 5 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1
|
||||
20 6 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1
|
||||
21 7 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1
|
||||
22 8 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1
|
||||
23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1
|
||||
24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1
|
||||
25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1
|
||||
26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
5 3.1575
|
||||
6 3.1575
|
||||
7 3.1575
|
||||
8 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.5974293795290144 -0.47217734566783476 0.1149860099192362 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.3607975285447209 -0.8084200276362509 0.5005631273908187 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.1880165420620915 -0.9339012982528754 0.9372222930006777 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.18789028377909187 -0.8807473585891459 1.3080750447260532 1 1 3.7269849963023267 0 0 0
|
||||
5 5 0.46680288593900887 -0.6314504249974493 1.6544618495816525 1 1 3.7269849963023267 0 0 0
|
||||
6 6 0.6156490001978658 -0.24344915610488765 1.9998398114466447 1 1 3.7269849963023267 0 0 0
|
||||
7 7 0.5475869309223161 0.10633006738807783 2.395688109397028 1 1 3.7269849963023267 0 0 0
|
||||
8 8 0.3964561058464781 0.33864915662119616 2.855380256681012 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.09151778690925949 0.33572177117709545 3.2793107140407853 1 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.260700239272384 0.23452584272483473 3.622064753017485 1 1 3.7269849963023267 0 0 0
|
||||
11 7 -0.44049173083867876 -0.04240311520575983 4.057361772274168 1 1 3.7269849963023267 0 0 0
|
||||
12 8 -0.48111471327910416 -0.3913669550617015 4.465217350523367 1 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.3029890593292223 -0.6218232516387349 4.889919411438907 1 1 3.7269849963023267 0 0 0
|
||||
14 4 0.36538593166250877 0.467104033114044 4.885957202043727 2 1 3.7269849963023267 0 0 0
|
||||
15 5 0.5837256243756591 0.1432569770282543 4.587937684834979 2 1 3.7269849963023267 0 0 0
|
||||
16 6 0.7270895848434721 -0.21648156960230241 4.19127441749994 2 1 3.7269849963023267 0 0 0
|
||||
17 3 0.5694364623788377 -0.5971020505771416 3.7905394408535833 2 1 3.7269849963023267 0 0 0
|
||||
18 4 0.32183479629572403 -0.7826674384502239 3.3981789941001397 2 1 3.7269849963023267 0 0 0
|
||||
19 5 0.027943077828669855 -0.8173952163019756 2.892497591992246 2 1 3.7269849963023267 0 0 0
|
||||
20 6 -0.34389471043742403 -0.6801076538339801 2.6010059142333977 2 1 3.7269849963023267 0 0 0
|
||||
21 7 -0.5722337592890715 -0.31543771192866543 2.2496367888009035 2 1 3.7269849963023267 0 0 0
|
||||
22 8 -0.5243059431454682 -0.018794840926191582 1.6669602274961965 2 1 3.7269849963023267 0 0 0
|
||||
23 1 -0.4467049661654279 0.15318137385858244 1.1669311078565738 2 1 3.7269849963023267 0 0 0
|
||||
24 2 -0.04279541944801792 0.24071675674438053 0.7924196804793574 2 1 3.7269849963023267 0 0 0
|
||||
25 3 0.33688934798342335 0.1390449738629785 0.42004977704361546 2 1 3.7269849963023267 0 0 0
|
||||
26 4 0.5381606093378432 -0.28366941895261566 0.04905784853961178 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 -0.1420563695014878 -0.2339928257547227 0.1871716305399088 -0.046333854442252194 0.08160574816172744 0.2791824603833533
|
||||
2 0.03390382747481304 0.2912921705525512 -0.1828986721885175 0.09422531767061365 -0.044398236946770545 0.011069519340877812
|
||||
3 0.05351747745964457 -0.3700026678535097 -0.01469442373794632 0.10875858697088675 0.2373869034785703 0.15028498953263314
|
||||
4 0.1107696836820372 0.012571134739153464 0.23554381030898286 0.11411649786729211 -0.23899527406990237 0.11196343804383825
|
||||
5 0.21949033826324368 -0.4153000294565104 0.18426481814713022 0.2497206165366295 0.2505624077277829 -0.35347918243093
|
||||
6 -0.24019769428878804 -0.16423570219236758 -0.003762466815720382 0.062008045889015595 0.22340307597010978 -0.38223196779931135
|
||||
7 0.12372477399377596 0.10393016373901434 0.08008946447311854 -0.15063203100274558 0.08544129561789665 -0.3233996805084572
|
||||
8 0.03216353270652909 -0.1291938805451393 0.1736283537356162 -0.17577447248216746 0.11132849782859955 -0.13659117762014125
|
||||
9 0.016485625003622013 0.01204732455105311 0.012268845318149781 -0.10829791072979295 0.1325154323216732 0.061321711941405295
|
||||
10 -0.10017034720683878 -0.09274368063499111 0.0712704971413183 -0.08539556363371427 -0.10194584018083674 0.12395163271335013
|
||||
11 0.1553620769751766 -0.017877616757193807 -0.1679552227127468 -0.11302061465460307 0.10833285249943261 -0.29004856929349787
|
||||
12 -0.25308607960176693 0.05651778438229357 -0.28293751231512154 0.08875447438401544 -0.0424858854741496 0.4807657704475166
|
||||
13 -0.006525152792083277 0.05278468067247092 0.0923614993309851 -0.17068957621149589 -0.21396827821680875 -0.22336174340467796
|
||||
14 -0.09024428084565417 0.19407821508904713 -0.27279958154128003 0.16579397498898726 0.05605196163049078 0.18139063086724955
|
||||
15 0.2329539015603435 0.08926675461196792 0.01755751945261716 0.14895763843533014 0.05566424996653055 0.038429304115211504
|
||||
16 -0.012766107314323394 -0.05870276075293287 0.22459362070331024 -0.051898555487544795 0.11349183901118838 -0.35625338947479507
|
||||
17 -0.20400754456760709 -0.43178141581578006 -0.05213026263746946 -0.16561150375144387 -0.08257869123336893 -0.31368221607714253
|
||||
18 0.26408469209202234 0.004101215813165573 -0.11409222616552296 -0.37751548716793587 0.021230702354981583 0.23218952685038605
|
||||
19 -0.2811352347889802 0.25474603468997514 0.0038005485218010606 0.2164466860189806 -0.3924452117278991 0.22754829879548555
|
||||
20 -0.34129793271588454 0.05074672818229578 -0.03388446943745919 -0.1368254010552013 -0.1547809974693013 -0.03266259795645136
|
||||
21 -0.25700758391191114 0.04693154859703793 0.08362546455733241 -0.08661574368141227 -0.030723569920460755 -0.18740437515161282
|
||||
22 0.08529314327765061 0.10662056255177826 -0.0742729015142829 -0.4671828719407557 -0.19246067344838313 0.20137866804242557
|
||||
23 -0.09337250162399305 -0.1907111010034805 0.19278254253312255 0.017795209772695803 -0.36506106427644847 0.24972052729172167
|
||||
24 -0.16063305395742022 0.12278800901705311 0.0513923554335936 -0.09716260028970423 -0.26401680055506943 0.08202659665577536
|
||||
25 -0.14736287972598905 0.09699085150412592 -0.20751532907712478 0.05612191742480806 -0.13929212905625324 0.034890079586931765
|
||||
26 -0.060417626533246734 0.35551862988152244 -0.19673503245092067 0.014766691426271806 0.02762183997756995 -0.20597323908506235
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00
|
||||
17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00
|
||||
18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00
|
||||
19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00
|
||||
20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00
|
||||
21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00
|
||||
22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00
|
||||
23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00
|
||||
24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00
|
||||
25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00
|
||||
26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9970278940278272 0.0014876174054512252 0.0750547523448584 0.017319055267040844
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9059171712388804 0.007913225291438054 0.04634256838354512 0.42083705406683053
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.7657426991864452 0.028071560533125216 0.13224385975981257 0.6287779160305484
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5238981696613685 0.0516703526741727 0.1609645534282743 0.8348360887142046
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.30973290897949424 0.0750672191209306 0.23962885621884192 0.9170651279902646
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.050269263744563454 0.08142241031464711 0.09584085715741358 0.9907865170259763
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.3805122714271814 0.08965734720629535 0.057827749665601925 0.9186010683391725
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.6066322463100545 0.015286960797006149 0.035984536832974555 0.7940206166563465
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.771660293819677 0.02607541526374929 -0.08047223278265907 -0.6303845520092687
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.9119628434851113 0.03686258000931541 -0.11017000132786052 -0.3934812487336936
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 0.9917294290821066 0.05835078551401739 -0.08073737536574405 -0.08092837290732445
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 0.9763527785523285 0.06753089597617556 0.004847281702108697 0.205307899901351
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 0.8553397145502984 0.1399133966151149 0.07233200118835512 0.49354462388392356
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.014416326682630282 -0.533642571147991 0.8442695396252617 0.04718813669228716
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 0.14095892784917538 -0.2201285495070387 0.9406003462562982 -0.21666792788520955
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 0.07323967796304806 0.05035907488974361 0.963136526452943 -0.2539053850556888
|
||||
17 1.173984503142341 1.173984503142341 1.173984503142341 0.030254986187638885 0.39195467212588947 0.9164794947567249 -0.07430684019611289
|
||||
18 1.173984503142341 1.173984503142341 1.173984503142341 -0.03080283760241768 0.6526511470205414 0.7481495879677094 -0.11562810865943304
|
||||
19 1.173984503142341 1.173984503142341 1.173984503142341 -0.09450197979153381 0.7469150592813072 0.6556128255138505 -0.0579576833217777
|
||||
20 1.173984503142341 1.173984503142341 1.173984503142341 -0.12903334341475137 0.9222523214328698 0.3501336268694509 -0.10103214950765672
|
||||
21 1.173984503142341 1.173984503142341 1.173984503142341 -0.0069954457806870336 0.9888131084284681 -0.09413955816471489 -0.11548785185859346
|
||||
22 1.173984503142341 1.173984503142341 1.173984503142341 0.029336230851923526 0.9805894852440379 -0.19236800606724952 -0.02404573205262194
|
||||
23 1.173984503142341 1.173984503142341 1.173984503142341 0.03080980270092377 0.872234086776475 -0.4869211139732921 0.03415088124407873
|
||||
24 1.173984503142341 1.173984503142341 1.173984503142341 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672
|
||||
25 1.173984503142341 1.173984503142341 1.173984503142341 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346
|
||||
26 1.173984503142341 1.173984503142341 1.173984503142341 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467
|
||||
|
||||
@ -1,10 +1,11 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
variable number equal 4
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable ntype equal 4
|
||||
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -14,20 +15,21 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
@ -52,28 +54,19 @@ jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -84,14 +77,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
@ -1,10 +1,11 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
variable number equal 8
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -14,20 +15,21 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
|
||||
group all type 1 8
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
@ -52,28 +54,19 @@ jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -84,14 +77,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,244 +0,0 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 4
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.876675896491307 | erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211
|
||||
20000 ekin = 1.02178060459022 | erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121
|
||||
30000 ekin = 1.77819697871127 | erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565
|
||||
40000 ekin = 2.55095642638533 | erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372
|
||||
50000 ekin = 2.43321388920862 | erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264
|
||||
60000 ekin = 2.51123200110303 | erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791
|
||||
70000 ekin = 3.33444097207872 | erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404
|
||||
80000 ekin = 3.41969296989344 | erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023
|
||||
90000 ekin = 3.53106755106414 | erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497
|
||||
100000 ekin = 3.47860763041501 | erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413
|
||||
100000 0.09276287 -1.4972391 0.050590991 -1.3128555 0.00017815014
|
||||
Loop time of 7.33046 on 1 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 117864.395 tau/day, 13641.712 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.4814 | 6.4814 | 6.4814 | 0.0 | 88.42
|
||||
Bond | 0.16262 | 0.16262 | 0.16262 | 0.0 | 2.22
|
||||
Neigh | 4.2e-05 | 4.2e-05 | 4.2e-05 | 0.0 | 0.00
|
||||
Comm | 0.019555 | 0.019555 | 0.019555 | 0.0 | 0.27
|
||||
Output | 0.00131 | 0.00131 | 0.00131 | 0.0 | 0.02
|
||||
Modify | 0.64596 | 0.64596 | 0.64596 | 0.0 | 8.81
|
||||
Other | | 0.01961 | | | 0.27
|
||||
|
||||
Nlocal: 26.0 ave 26.0 max 26.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 299.0 ave 299.0 max 299.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 299
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:07
|
||||
@ -1,244 +0,0 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 4
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.705506935391957 | erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106
|
||||
20000 ekin = 1.16547426389222 | erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755
|
||||
30000 ekin = 2.07592540045025 | erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902
|
||||
40000 ekin = 3.0352692177735 | erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022
|
||||
50000 ekin = 2.69044710203348 | erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511
|
||||
60000 ekin = 2.90956639769978 | erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784
|
||||
70000 ekin = 1.89941118514544 | erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529
|
||||
80000 ekin = 2.43472912058895 | erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883
|
||||
90000 ekin = 2.3759389593227 | erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149
|
||||
100000 ekin = 3.23901515322217 | erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778
|
||||
100000 0.086373737 -1.5432369 0.057459797 -1.3611996 7.7958353e-05
|
||||
Loop time of 6.09292 on 4 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 141803.976 tau/day, 16412.497 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.047712 | 2.5625 | 5.2874 | 157.3 | 42.06
|
||||
Bond | 0.007398 | 0.053166 | 0.10097 | 19.8 | 0.87
|
||||
Neigh | 1.8e-05 | 1.8e-05 | 1.8e-05 | 0.0 | 0.00
|
||||
Comm | 0.29205 | 2.9624 | 5.4188 | 143.0 | 48.62
|
||||
Output | 0.000866 | 0.00099325 | 0.001303 | 0.0 | 0.02
|
||||
Modify | 0.016247 | 0.18354 | 0.37524 | 39.2 | 3.01
|
||||
Other | | 0.3303 | | | 5.42
|
||||
|
||||
Nlocal: 6.5 ave 14.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 18.5 ave 24.0 max 12.0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 113.75 ave 239.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 455
|
||||
Ave neighs/atom = 17.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -1,286 +0,0 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 8
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 5%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 5+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 6%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 6+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 6 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 6 7 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 7%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 8%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.876675896491307 | erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211
|
||||
20000 ekin = 1.02178060459022 | erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121
|
||||
30000 ekin = 1.77819697871127 | erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565
|
||||
40000 ekin = 2.55095642638533 | erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372
|
||||
50000 ekin = 2.43321388920862 | erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264
|
||||
60000 ekin = 2.51123200110303 | erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791
|
||||
70000 ekin = 3.33444097207872 | erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404
|
||||
80000 ekin = 3.41969296989344 | erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023
|
||||
90000 ekin = 3.53106755106414 | erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497
|
||||
100000 ekin = 3.47860763041501 | erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413
|
||||
100000 0.09276287 -1.4972391 0.050590991 -1.3128555 0.00017815014
|
||||
Loop time of 7.44606 on 1 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 116034.458 tau/day, 13429.914 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.5843 | 6.5843 | 6.5843 | 0.0 | 88.43
|
||||
Bond | 0.16149 | 0.16149 | 0.16149 | 0.0 | 2.17
|
||||
Neigh | 4.3e-05 | 4.3e-05 | 4.3e-05 | 0.0 | 0.00
|
||||
Comm | 0.022595 | 0.022595 | 0.022595 | 0.0 | 0.30
|
||||
Output | 0.001492 | 0.001492 | 0.001492 | 0.0 | 0.02
|
||||
Modify | 0.65313 | 0.65313 | 0.65313 | 0.0 | 8.77
|
||||
Other | | 0.02299 | | | 0.31
|
||||
|
||||
Nlocal: 26.0 ave 26.0 max 26.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 299.0 ave 299.0 max 299.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 299
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:07
|
||||
@ -1,286 +0,0 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 8
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 5%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 5+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 6%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 6+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 6 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 6 7 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 7%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 8%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.705506935391957 | erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106
|
||||
20000 ekin = 1.16547426389222 | erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755
|
||||
30000 ekin = 2.07592540045025 | erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902
|
||||
40000 ekin = 3.0352692177735 | erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022
|
||||
50000 ekin = 2.69044710203348 | erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511
|
||||
60000 ekin = 2.90956639769978 | erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784
|
||||
70000 ekin = 1.89941118514544 | erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529
|
||||
80000 ekin = 2.43472912058895 | erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883
|
||||
90000 ekin = 2.3759389593227 | erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149
|
||||
100000 ekin = 3.23901515322217 | erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778
|
||||
100000 0.086373737 -1.5432369 0.057459797 -1.3611996 7.7958353e-05
|
||||
Loop time of 6.15993 on 4 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 140261.437 tau/day, 16233.963 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.049533 | 2.573 | 5.3124 | 157.6 | 41.77
|
||||
Bond | 0.007709 | 0.055244 | 0.10383 | 20.2 | 0.90
|
||||
Neigh | 1.8e-05 | 1.875e-05 | 1.9e-05 | 0.0 | 0.00
|
||||
Comm | 0.32774 | 3.0114 | 5.4815 | 142.5 | 48.89
|
||||
Output | 0.000925 | 0.0010595 | 0.00137 | 0.6 | 0.02
|
||||
Modify | 0.016369 | 0.18492 | 0.37491 | 39.3 | 3.00
|
||||
Other | | 0.3343 | | | 5.43
|
||||
|
||||
Nlocal: 6.5 ave 14.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 18.5 ave 24.0 max 12.0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 113.75 ave 239.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 455
|
||||
Ave neighs/atom = 17.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
91
examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2
Normal file
91
examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2
Normal file
@ -0,0 +1,91 @@
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
16 atoms
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0
|
||||
14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0
|
||||
15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0
|
||||
16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725
|
||||
2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215
|
||||
3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625
|
||||
4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877
|
||||
5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292
|
||||
6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776
|
||||
7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357
|
||||
8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032
|
||||
9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696
|
||||
10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506
|
||||
11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418
|
||||
12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697
|
||||
13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132
|
||||
14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759
|
||||
15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106
|
||||
16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
@ -1,7 +1,8 @@
|
||||
variable number equal 4
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.5
|
||||
|
||||
units lj
|
||||
|
||||
@ -11,14 +12,14 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex4
|
||||
read_data data.duplex2
|
||||
|
||||
set atom * mass 3.1575
|
||||
|
||||
@ -31,38 +32,27 @@ special_bonds lj 0 1 1
|
||||
|
||||
# oxRNA2 pair interactions
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
|
||||
pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxrna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
|
||||
pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
|
||||
pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
|
||||
pair_coeff * * oxrna2/dh ${T} 0.5 1.02455
|
||||
pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -73,10 +63,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,96 +0,0 @@
|
||||
# LAMMPS data file
|
||||
16 atoms
|
||||
16 ellipsoids
|
||||
13 bonds
|
||||
|
||||
4 atom types
|
||||
1 bond types
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
|
||||
7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
|
||||
10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
|
||||
11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
|
||||
12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
|
||||
13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
|
||||
14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user