Updated documentation
This commit is contained in:
Oliver Henrich
@ -1,8 +1,12 @@
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This directory contains example data and input files
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and utility scripts for the oxDNA coarse-grained model
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for DNA.
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as well as utility scripts for the oxDNA/oxDNA2/oxRNA2
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coarse-grained model for DNA and RNA.
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/******************************************************************************/
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/examples/oxDNA/duplex1:
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/examples/oxDNA2/duplex1:
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/examples/duplex1:
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Input, data and log files for a DNA duplex (double-stranded DNA)
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consisiting of 5 base pairs. The duplex contains two strands with
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complementary base pairs. The topology is
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@ -11,7 +15,14 @@ A - C - G - T - A
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T - G - C - A - T
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/examples/duplex2:
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Note that in this example the stacking and hydrogen-bonding interactions
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are sequence-averaged (cf. keyword 'seqav' in according pair styles).
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/******************************************************************************/
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/examples/oxDNA/duplex2:
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/examples/oxDNA2/duplex2:
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Input, data and log files for a nicked DNA duplex (double-stranded DNA)
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consisiting of 8 base pairs. The duplex contains strands with
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complementary base pairs, but the backbone on one side is not continuous:
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@ -22,9 +33,15 @@ A - C - G - T - A - C - G - T
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T - G - C - A T - G - C - A
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/examples/duplex3:
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This is basically the duplex1 run with sequence-dependent stacking
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and hydrogen-bonding strengths enabled and both nucleotide mass and
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Note that in this example the stacking and hydrogen-bonding interactions
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are sequence-averaged (cf. keyword 'seqav' in according pair styles).
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/******************************************************************************/
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/examples/oxDNA2/duplex3:
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This is the duplex1 run with sequence-dependent stacking and
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hydrogen-bonding strengths enabled and both nucleotide mass and
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moment of inertia set to the value of the standalone implementation
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of oxDNA (M = I = 1). To achieve this, the masses can be set directly
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in the input and data file, whereas the moment of inertia is set via
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@ -33,6 +50,19 @@ The change of mass and moment of inertia allows direct comparision of
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e.g. trajectory data, energies or time-dependent observables on a per-timestep
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basis until numerical noise causes deviations at later simulation times.
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As mentioned above, the stacking and hydrogen-bonding interactions
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are sequence-dependent (cf. keyword 'seqdep' in according pair styles).
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/******************************************************************************/
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/examples/oxRNA2/duplex4
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This is the duplex2 run with the oxRNA2 force field instead of the oxDNA or
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oxDNA2 force field and sequence-dependent stacking and hydrogen-bonding
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strengths enabled.
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/******************************************************************************/
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/util:
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This directory contains a simple python setup tool which creates
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single straight or helical DNA strands, DNA duplexes or arrays of DNA
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@ -1,4 +1,4 @@
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variable number equal 1
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variable number equal 3
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variable ofreq equal 1000
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variable efreq equal 1000
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variable T equal 0.1
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@ -1,5 +1,5 @@
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LAMMPS (7 Aug 2019)
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variable number equal 1
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variable number equal 3
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variable ofreq equal 1000
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variable efreq equal 1000
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variable T equal 0.1
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@ -1,5 +1,5 @@
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LAMMPS (7 Aug 2019)
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variable number equal 1
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variable number equal 3
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variable ofreq equal 1000
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variable efreq equal 1000
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variable T equal 0.1
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96
examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4
Normal file
96
examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4
Normal file
@ -0,0 +1,96 @@
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# LAMMPS data file
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16 atoms
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16 ellipsoids
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13 bonds
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4 atom types
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1 bond types
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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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Masses
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1 3.1575
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2 3.1575
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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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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 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
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7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
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8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
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9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
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10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
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11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
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12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
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13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
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14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
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15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
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16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
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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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11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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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 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
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7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
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8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
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9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
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10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
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11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
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12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
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13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
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14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
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15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
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16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 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 5 6
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6 1 6 7
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7 1 7 8
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8 1 9 10
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9 1 10 11
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10 1 11 12
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11 1 13 14
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12 1 14 15
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13 1 15 16
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80
examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4
Normal file
80
examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4
Normal file
@ -0,0 +1,80 @@
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variable number equal 4
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variable ofreq equal 1000
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variable efreq equal 1000
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variable T equal 0.1
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units lj
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dimension 3
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newton off
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boundary p p p
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atom_style hybrid bond ellipsoid
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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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neigh_modify every 1 delay 0 check yes
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read_data data.duplex4
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set atom * mass 3.1575
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group all type 1 4
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# oxRNA2 bond interactions - FENE backbone
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bond_style oxrna2/fene
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bond_coeff * 2.0 0.25 0.761070781051
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# oxRNA2 pair interactions
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pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
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pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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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
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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
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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
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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
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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
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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
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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
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pair_coeff * * oxrna2/dh ${T} 0.5 1.02455
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# NVE ensemble
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#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
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#fix 1 all nve/dot
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fix 1 all nve/asphere
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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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#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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#dump pos all xyz ${ofreq} traj.${number}.xyz
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#compute quat all property/atom quatw quati quatj quatk
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#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
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#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
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compute erot all erotate/asphere
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compute ekin all ke
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compute epot all pe
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variable erot equal c_erot
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variable ekin equal c_ekin
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variable epot equal c_epot
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variable etot equal c_erot+c_ekin+c_epot
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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
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#dump_modify out sort id
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#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"
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run 1000000
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#write_restart config.${number}.*
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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