rename some examples folders
This commit is contained in:
Axel Kohlmeyer
58
examples/USER-MISC/imd/README
Normal file
58
examples/USER-MISC/imd/README
Normal file
@ -0,0 +1,58 @@
|
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Interactive MD example files using the fix imd command
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To run the demos, first start the LAMMPS simulation, during
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initialization it will stop and wait for an IMD client to
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connect. Then launch VMD on the same machine with the respective
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script to connect and visualize the running simulation. For example:
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mpirun -np 4 lmp_linux -log none -in in.melt_imd &
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vmd -e melt_imd-demo.vmd
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When exiting VMD, the simulation will either continue or wait
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for a new connection depending on whether the "nowait" flag was
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activated or not. To terminate the LAMMPS simulation,
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type "imd kill" into the VMD command line prompt.
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To combine interactive MD with force feedback using a
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Novint Falcon game controller, have a look at:
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http://sites.google.com/site/akohlmey/software/vrpn-icms
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Examples:
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melt:
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an adapted version of the 3d-LJ melt example.
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the VMD visualization contains one highlighted
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atom to play with force application through a
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mouse: Open the Graphical Representations dialog,
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Double-click on the first VDW representation
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to disable it, click with the mouse on the blue
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atom and - while holding the mouse button down -
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drag the atom into some direction. A red arrow
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should appear indicating direction and magnitude
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of the force. Now double-click on the first VDW
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representation again to re-enable the rest of
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the atoms and watch the blue atom move.
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bucky-plus-cnt:
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this is "the buckyball challenge". a demo that
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is very popular to demonstrate the use of IMD
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with force feedback. The system is a SWCNT with
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some atoms fixed in space and five C60 fullerenes
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in a reflecting wall box. The challenge is to
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push all five buckyballs into the nanotube and
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have them stay inside.
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deca-ala-solv:
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a solvated deca alanin helix. The mouse mode is
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preset to move residues instead of individual
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atoms. Disable the water rep and grab an atom
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from the peptide and drag it to apply forces.
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deca-ala:
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this is the same system as the previous, but
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the fix is only applied to the peptide and thus
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the corresponding VMD script needs a different
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topology file with the matching number of atoms
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to visualize it and receive the IMD data.
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In case of problems, contact <akohlmey@gmail.com>.
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5421
examples/USER-MISC/imd/bucky-plus-cnt-mol.psf
Normal file
5421
examples/USER-MISC/imd/bucky-plus-cnt-mol.psf
Normal file
File diff suppressed because it is too large
Load Diff
43
examples/USER-MISC/imd/bucky_cnt_imd.vmd
Normal file
43
examples/USER-MISC/imd/bucky_cnt_imd.vmd
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#!/usr/local/bin/vmd
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# Display settings
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display projection Perspective
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mol new bucky-plus-cnt-mol.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
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mol delrep 0 top
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mol representation Licorice 0.3 10.0 10.0
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mol color ColorID 7
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mol selection {index >= 300}
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mol addrep top
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mol selection {index < 300}
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mol color ColorID 23
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mol material Glossy
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mol representation VDW 0.600000 15.000000
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mol addrep top
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mol rename top {Put the balls into the tube}
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draw delete all
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draw material AOChalky
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draw color gray
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draw triangle {-36.0 -31.0 -7.0} { 46.0 -31.0 -7.0} { 46.0 31.0 -7.0}
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draw triangle {-36.0 -31.0 -7.0} {-36.0 31.0 -7.0} { 46.0 31.0 -7.0}
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draw color red
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draw triangle {-36.0 -31.0 -7.0} {-36.0 -31.0 7.0} {-36.0 31.0 7.0}
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draw triangle {-36.0 -31.0 -7.0} {-36.0 31.0 -7.0} {-36.0 31.0 7.0}
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draw triangle { 46.0 -31.0 -7.0} { 46.0 -31.0 7.0} { 46.0 31.0 7.0}
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draw triangle { 46.0 -31.0 -7.0} { 46.0 31.0 -7.0} { 46.0 31.0 7.0}
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draw triangle {-36.0 -31.0 -7.0} {-36.0 -31.0 7.0} { 46.0 -31.0 7.0}
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draw triangle {-36.0 -31.0 -7.0} { 46.0 -31.0 -7.0} { 46.0 -31.0 7.0}
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draw triangle {-36.0 31.0 -7.0} {-36.0 31.0 7.0} { 46.0 31.0 7.0}
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draw triangle {-36.0 31.0 -7.0} { 46.0 31.0 -7.0} { 46.0 31.0 7.0}
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imd connect localhost 6789
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after idle {
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global env
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set env(VMDFULLSCREEN) 1
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display resize 1200 900
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rotate x by -5
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rotate y by -5
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axes location off
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}
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11287
examples/USER-MISC/imd/data.bucky-plus-cnt
Normal file
11287
examples/USER-MISC/imd/data.bucky-plus-cnt
Normal file
File diff suppressed because it is too large
Load Diff
21892
examples/USER-MISC/imd/data.deca-ala-solv
Normal file
21892
examples/USER-MISC/imd/data.deca-ala-solv
Normal file
File diff suppressed because it is too large
Load Diff
10178
examples/USER-MISC/imd/deca-ala-solv.psf
Normal file
10178
examples/USER-MISC/imd/deca-ala-solv.psf
Normal file
File diff suppressed because it is too large
Load Diff
28
examples/USER-MISC/imd/deca-ala-solv_imd-demo.vmd
Normal file
28
examples/USER-MISC/imd/deca-ala-solv_imd-demo.vmd
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@ -0,0 +1,28 @@
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#!/usr/local/bin/vmd
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# Display settings
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display projection Orthographic
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mol new deca-ala-solv.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
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mol delrep 0 top
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mol representation Licorice
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mol color Name
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mol selection {protein}
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mol material Glossy
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mol addrep top
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mol selupdate 0 top 1
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mol representation HBonds 4.000000 30.000000 3.000000
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mol color ColorID 4
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mol selection {same residue as within 3.1 of protein}
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mol material Opaque
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mol addrep top
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mol selupdate 1 top 1
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mol representation Lines 2.000000
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mol color Name
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mol selection {(same residue as within 3.1 of protein) and water}
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mol addrep top
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mol selupdate 2 top 1
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imd connect localhost 5678
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sleep 1
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display resetview
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mouse mode forceres
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370
examples/USER-MISC/imd/deca-ala.psf
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370
examples/USER-MISC/imd/deca-ala.psf
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@ -0,0 +1,370 @@
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PSF
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6 !NTITLE
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REMARKS original generated structure x-plor psf file
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REMARKS 2 patches were applied to the molecule.
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REMARKS topology top_all22_prot.rtf
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REMARKS segment DAL { first NTER; last CTER; auto angles dihedrals }
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REMARKS defaultpatch NTER DAL:1
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REMARKS defaultpatch CTER DAL:10
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103 !NATOM
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1 DAL 1 ALA N NH3 -0.300000 14.0070 0
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2 DAL 1 ALA HT1 HC 0.330000 1.0080 0
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3 DAL 1 ALA HT2 HC 0.330000 1.0080 0
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||||
4 DAL 1 ALA HT3 HC 0.330000 1.0080 0
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||||
5 DAL 1 ALA CA CT1 0.210000 12.0110 0
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||||
6 DAL 1 ALA HA HB 0.100000 1.0080 0
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||||
7 DAL 1 ALA CB CT3 -0.270000 12.0110 0
|
||||
8 DAL 1 ALA HB1 HA 0.090000 1.0080 0
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||||
9 DAL 1 ALA HB2 HA 0.090000 1.0080 0
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||||
10 DAL 1 ALA HB3 HA 0.090000 1.0080 0
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||||
11 DAL 1 ALA C C 0.510000 12.0110 0
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||||
12 DAL 1 ALA O O -0.510000 15.9990 0
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13 DAL 2 ALA N NH1 -0.470000 14.0070 0
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||||
14 DAL 2 ALA HN H 0.310000 1.0080 0
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15 DAL 2 ALA CA CT1 0.070000 12.0110 0
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16 DAL 2 ALA HA HB 0.090000 1.0080 0
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17 DAL 2 ALA CB CT3 -0.270000 12.0110 0
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18 DAL 2 ALA HB1 HA 0.090000 1.0080 0
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19 DAL 2 ALA HB2 HA 0.090000 1.0080 0
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20 DAL 2 ALA HB3 HA 0.090000 1.0080 0
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21 DAL 2 ALA C C 0.510000 12.0110 0
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22 DAL 2 ALA O O -0.510000 15.9990 0
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23 DAL 3 ALA N NH1 -0.470000 14.0070 0
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24 DAL 3 ALA HN H 0.310000 1.0080 0
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25 DAL 3 ALA CA CT1 0.070000 12.0110 0
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26 DAL 3 ALA HA HB 0.090000 1.0080 0
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27 DAL 3 ALA CB CT3 -0.270000 12.0110 0
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||||
28 DAL 3 ALA HB1 HA 0.090000 1.0080 0
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29 DAL 3 ALA HB2 HA 0.090000 1.0080 0
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30 DAL 3 ALA HB3 HA 0.090000 1.0080 0
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31 DAL 3 ALA C C 0.510000 12.0110 0
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32 DAL 3 ALA O O -0.510000 15.9990 0
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33 DAL 4 ALA N NH1 -0.470000 14.0070 0
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34 DAL 4 ALA HN H 0.310000 1.0080 0
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35 DAL 4 ALA CA CT1 0.070000 12.0110 0
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36 DAL 4 ALA HA HB 0.090000 1.0080 0
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37 DAL 4 ALA CB CT3 -0.270000 12.0110 0
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||||
38 DAL 4 ALA HB1 HA 0.090000 1.0080 0
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39 DAL 4 ALA HB2 HA 0.090000 1.0080 0
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40 DAL 4 ALA HB3 HA 0.090000 1.0080 0
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||||
41 DAL 4 ALA C C 0.510000 12.0110 0
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42 DAL 4 ALA O O -0.510000 15.9990 0
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||||
43 DAL 5 ALA N NH1 -0.470000 14.0070 0
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44 DAL 5 ALA HN H 0.310000 1.0080 0
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||||
45 DAL 5 ALA CA CT1 0.070000 12.0110 0
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||||
46 DAL 5 ALA HA HB 0.090000 1.0080 0
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||||
47 DAL 5 ALA CB CT3 -0.270000 12.0110 0
|
||||
48 DAL 5 ALA HB1 HA 0.090000 1.0080 0
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||||
49 DAL 5 ALA HB2 HA 0.090000 1.0080 0
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||||
50 DAL 5 ALA HB3 HA 0.090000 1.0080 0
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||||
51 DAL 5 ALA C C 0.510000 12.0110 0
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||||
52 DAL 5 ALA O O -0.510000 15.9990 0
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||||
53 DAL 6 ALA N NH1 -0.470000 14.0070 0
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||||
54 DAL 6 ALA HN H 0.310000 1.0080 0
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||||
55 DAL 6 ALA CA CT1 0.070000 12.0110 0
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||||
56 DAL 6 ALA HA HB 0.090000 1.0080 0
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||||
57 DAL 6 ALA CB CT3 -0.270000 12.0110 0
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||||
58 DAL 6 ALA HB1 HA 0.090000 1.0080 0
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||||
59 DAL 6 ALA HB2 HA 0.090000 1.0080 0
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||||
60 DAL 6 ALA HB3 HA 0.090000 1.0080 0
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||||
61 DAL 6 ALA C C 0.510000 12.0110 0
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||||
62 DAL 6 ALA O O -0.510000 15.9990 0
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||||
63 DAL 7 ALA N NH1 -0.470000 14.0070 0
|
||||
64 DAL 7 ALA HN H 0.310000 1.0080 0
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||||
65 DAL 7 ALA CA CT1 0.070000 12.0110 0
|
||||
66 DAL 7 ALA HA HB 0.090000 1.0080 0
|
||||
67 DAL 7 ALA CB CT3 -0.270000 12.0110 0
|
||||
68 DAL 7 ALA HB1 HA 0.090000 1.0080 0
|
||||
69 DAL 7 ALA HB2 HA 0.090000 1.0080 0
|
||||
70 DAL 7 ALA HB3 HA 0.090000 1.0080 0
|
||||
71 DAL 7 ALA C C 0.510000 12.0110 0
|
||||
72 DAL 7 ALA O O -0.510000 15.9990 0
|
||||
73 DAL 8 ALA N NH1 -0.470000 14.0070 0
|
||||
74 DAL 8 ALA HN H 0.310000 1.0080 0
|
||||
75 DAL 8 ALA CA CT1 0.070000 12.0110 0
|
||||
76 DAL 8 ALA HA HB 0.090000 1.0080 0
|
||||
77 DAL 8 ALA CB CT3 -0.270000 12.0110 0
|
||||
78 DAL 8 ALA HB1 HA 0.090000 1.0080 0
|
||||
79 DAL 8 ALA HB2 HA 0.090000 1.0080 0
|
||||
80 DAL 8 ALA HB3 HA 0.090000 1.0080 0
|
||||
81 DAL 8 ALA C C 0.510000 12.0110 0
|
||||
82 DAL 8 ALA O O -0.510000 15.9990 0
|
||||
83 DAL 9 ALA N NH1 -0.470000 14.0070 0
|
||||
84 DAL 9 ALA HN H 0.310000 1.0080 0
|
||||
85 DAL 9 ALA CA CT1 0.070000 12.0110 0
|
||||
86 DAL 9 ALA HA HB 0.090000 1.0080 0
|
||||
87 DAL 9 ALA CB CT3 -0.270000 12.0110 0
|
||||
88 DAL 9 ALA HB1 HA 0.090000 1.0080 0
|
||||
89 DAL 9 ALA HB2 HA 0.090000 1.0080 0
|
||||
90 DAL 9 ALA HB3 HA 0.090000 1.0080 0
|
||||
91 DAL 9 ALA C C 0.510000 12.0110 0
|
||||
92 DAL 9 ALA O O -0.510000 15.9990 0
|
||||
93 DAL 10 ALA C CC 0.340000 12.0110 0
|
||||
94 DAL 10 ALA OT1 OC -0.670000 15.9990 0
|
||||
95 DAL 10 ALA OT2 OC -0.670000 15.9990 0
|
||||
96 DAL 10 ALA N NH1 -0.470000 14.0070 0
|
||||
97 DAL 10 ALA HN H 0.310000 1.0080 0
|
||||
98 DAL 10 ALA CA CT1 0.070000 12.0110 0
|
||||
99 DAL 10 ALA HA HB 0.090000 1.0080 0
|
||||
100 DAL 10 ALA CB CT3 -0.270000 12.0110 0
|
||||
101 DAL 10 ALA HB1 HA 0.090000 1.0080 0
|
||||
102 DAL 10 ALA HB2 HA 0.090000 1.0080 0
|
||||
103 DAL 10 ALA HB3 HA 0.090000 1.0080 0
|
||||
|
||||
102 !NBOND: bonds
|
||||
1 5 2 1 3 1 4 1
|
||||
5 6 7 5 7 8 7 9
|
||||
7 10 11 5 11 13 12 11
|
||||
13 14 13 15 15 16 17 15
|
||||
17 18 17 19 17 20 21 15
|
||||
21 23 22 21 23 24 23 25
|
||||
25 26 27 25 27 28 27 29
|
||||
27 30 31 25 31 33 32 31
|
||||
33 34 33 35 35 36 37 35
|
||||
37 38 37 39 37 40 41 35
|
||||
41 43 42 41 43 44 43 45
|
||||
45 46 47 45 47 48 47 49
|
||||
47 50 51 45 51 53 52 51
|
||||
53 54 53 55 55 56 57 55
|
||||
57 58 57 59 57 60 61 55
|
||||
61 63 62 61 63 64 63 65
|
||||
65 66 67 65 67 68 67 69
|
||||
67 70 71 65 71 73 72 71
|
||||
73 74 73 75 75 76 77 75
|
||||
77 78 77 79 77 80 81 75
|
||||
81 83 82 81 83 84 83 85
|
||||
85 86 87 85 87 88 87 89
|
||||
87 90 91 85 91 96 92 91
|
||||
93 95 93 94 93 98 96 97
|
||||
96 98 98 99 100 98 100 101
|
||||
100 102 100 103
|
||||
|
||||
183 !NTHETA: angles
|
||||
1 5 6 1 5 11 2 1 5
|
||||
2 1 4 2 1 3 3 1 5
|
||||
3 1 4 4 1 5 5 11 12
|
||||
5 11 13 5 7 10 5 7 9
|
||||
5 7 8 7 5 6 7 5 11
|
||||
7 5 1 8 7 10 8 7 9
|
||||
9 7 10 11 5 6 13 15 16
|
||||
13 15 21 13 11 12 14 13 11
|
||||
14 13 15 15 21 22 15 21 23
|
||||
15 17 20 15 17 19 15 17 18
|
||||
15 13 11 17 15 16 17 15 21
|
||||
17 15 13 18 17 20 18 17 19
|
||||
19 17 20 21 15 16 23 25 26
|
||||
23 25 31 23 21 22 24 23 21
|
||||
24 23 25 25 31 32 25 31 33
|
||||
25 27 30 25 27 29 25 27 28
|
||||
25 23 21 27 25 26 27 25 31
|
||||
27 25 23 28 27 30 28 27 29
|
||||
29 27 30 31 25 26 33 35 36
|
||||
33 35 41 33 31 32 34 33 31
|
||||
34 33 35 35 41 42 35 41 43
|
||||
35 37 40 35 37 39 35 37 38
|
||||
35 33 31 37 35 36 37 35 41
|
||||
37 35 33 38 37 40 38 37 39
|
||||
39 37 40 41 35 36 43 45 46
|
||||
43 45 51 43 41 42 44 43 41
|
||||
44 43 45 45 51 52 45 51 53
|
||||
45 47 50 45 47 49 45 47 48
|
||||
45 43 41 47 45 46 47 45 51
|
||||
47 45 43 48 47 50 48 47 49
|
||||
49 47 50 51 45 46 53 55 56
|
||||
53 55 61 53 51 52 54 53 51
|
||||
54 53 55 55 61 62 55 61 63
|
||||
55 57 60 55 57 59 55 57 58
|
||||
55 53 51 57 55 56 57 55 61
|
||||
57 55 53 58 57 60 58 57 59
|
||||
59 57 60 61 55 56 63 65 66
|
||||
63 65 71 63 61 62 64 63 61
|
||||
64 63 65 65 71 72 65 71 73
|
||||
65 67 70 65 67 69 65 67 68
|
||||
65 63 61 67 65 66 67 65 71
|
||||
67 65 63 68 67 70 68 67 69
|
||||
69 67 70 71 65 66 73 75 76
|
||||
73 75 81 73 71 72 74 73 71
|
||||
74 73 75 75 81 82 75 81 83
|
||||
75 77 80 75 77 79 75 77 78
|
||||
75 73 71 77 75 76 77 75 81
|
||||
77 75 73 78 77 80 78 77 79
|
||||
79 77 80 81 75 76 83 85 86
|
||||
83 85 91 83 81 82 84 83 81
|
||||
84 83 85 85 91 92 85 91 96
|
||||
85 87 90 85 87 89 85 87 88
|
||||
85 83 81 87 85 86 87 85 91
|
||||
87 85 83 88 87 90 88 87 89
|
||||
89 87 90 91 85 86 93 98 99
|
||||
94 93 98 95 93 98 95 93 94
|
||||
96 98 99 96 98 93 96 91 92
|
||||
97 96 91 97 96 98 98 100 103
|
||||
98 100 102 98 100 101 98 96 91
|
||||
100 98 99 100 98 93 100 98 96
|
||||
101 100 103 101 100 102 102 100 103
|
||||
|
||||
249 !NPHI: dihedrals
|
||||
1 5 7 8 1 5 7 9
|
||||
1 5 7 10 1 5 11 13
|
||||
1 5 11 12 2 1 5 7
|
||||
2 1 5 11 2 1 5 6
|
||||
3 1 5 7 3 1 5 11
|
||||
3 1 5 6 4 1 5 7
|
||||
4 1 5 11 4 1 5 6
|
||||
5 11 13 14 5 11 13 15
|
||||
6 5 7 8 6 5 7 9
|
||||
6 5 7 10 6 5 11 13
|
||||
6 5 11 12 7 5 11 13
|
||||
7 5 11 12 8 7 5 11
|
||||
9 7 5 11 10 7 5 11
|
||||
11 13 15 17 11 13 15 21
|
||||
11 13 15 16 12 11 13 14
|
||||
12 11 13 15 13 15 17 18
|
||||
13 15 17 19 13 15 17 20
|
||||
13 15 21 23 13 15 21 22
|
||||
14 13 15 17 14 13 15 21
|
||||
14 13 15 16 15 21 23 24
|
||||
15 21 23 25 16 15 17 18
|
||||
16 15 17 19 16 15 17 20
|
||||
16 15 21 23 16 15 21 22
|
||||
17 15 21 23 17 15 21 22
|
||||
18 17 15 21 19 17 15 21
|
||||
20 17 15 21 21 23 25 27
|
||||
21 23 25 31 21 23 25 26
|
||||
22 21 23 24 22 21 23 25
|
||||
23 25 27 28 23 25 27 29
|
||||
23 25 27 30 23 25 31 33
|
||||
23 25 31 32 24 23 25 27
|
||||
24 23 25 31 24 23 25 26
|
||||
25 31 33 34 25 31 33 35
|
||||
26 25 27 28 26 25 27 29
|
||||
26 25 27 30 26 25 31 33
|
||||
26 25 31 32 27 25 31 33
|
||||
27 25 31 32 28 27 25 31
|
||||
29 27 25 31 30 27 25 31
|
||||
31 33 35 37 31 33 35 41
|
||||
31 33 35 36 32 31 33 34
|
||||
32 31 33 35 33 35 37 38
|
||||
33 35 37 39 33 35 37 40
|
||||
33 35 41 43 33 35 41 42
|
||||
34 33 35 37 34 33 35 41
|
||||
34 33 35 36 35 41 43 44
|
||||
35 41 43 45 36 35 37 38
|
||||
36 35 37 39 36 35 37 40
|
||||
36 35 41 43 36 35 41 42
|
||||
37 35 41 43 37 35 41 42
|
||||
38 37 35 41 39 37 35 41
|
||||
40 37 35 41 41 43 45 47
|
||||
41 43 45 51 41 43 45 46
|
||||
42 41 43 44 42 41 43 45
|
||||
43 45 47 48 43 45 47 49
|
||||
43 45 47 50 43 45 51 53
|
||||
43 45 51 52 44 43 45 47
|
||||
44 43 45 51 44 43 45 46
|
||||
45 51 53 54 45 51 53 55
|
||||
46 45 47 48 46 45 47 49
|
||||
46 45 47 50 46 45 51 53
|
||||
46 45 51 52 47 45 51 53
|
||||
47 45 51 52 48 47 45 51
|
||||
49 47 45 51 50 47 45 51
|
||||
51 53 55 57 51 53 55 61
|
||||
51 53 55 56 52 51 53 54
|
||||
52 51 53 55 53 55 57 58
|
||||
53 55 57 59 53 55 57 60
|
||||
53 55 61 63 53 55 61 62
|
||||
54 53 55 57 54 53 55 61
|
||||
54 53 55 56 55 61 63 64
|
||||
55 61 63 65 56 55 57 58
|
||||
56 55 57 59 56 55 57 60
|
||||
56 55 61 63 56 55 61 62
|
||||
57 55 61 63 57 55 61 62
|
||||
58 57 55 61 59 57 55 61
|
||||
60 57 55 61 61 63 65 67
|
||||
61 63 65 71 61 63 65 66
|
||||
62 61 63 64 62 61 63 65
|
||||
63 65 67 68 63 65 67 69
|
||||
63 65 67 70 63 65 71 73
|
||||
63 65 71 72 64 63 65 67
|
||||
64 63 65 71 64 63 65 66
|
||||
65 71 73 74 65 71 73 75
|
||||
66 65 67 68 66 65 67 69
|
||||
66 65 67 70 66 65 71 73
|
||||
66 65 71 72 67 65 71 73
|
||||
67 65 71 72 68 67 65 71
|
||||
69 67 65 71 70 67 65 71
|
||||
71 73 75 77 71 73 75 81
|
||||
71 73 75 76 72 71 73 74
|
||||
72 71 73 75 73 75 77 78
|
||||
73 75 77 79 73 75 77 80
|
||||
73 75 81 83 73 75 81 82
|
||||
74 73 75 77 74 73 75 81
|
||||
74 73 75 76 75 81 83 84
|
||||
75 81 83 85 76 75 77 78
|
||||
76 75 77 79 76 75 77 80
|
||||
76 75 81 83 76 75 81 82
|
||||
77 75 81 83 77 75 81 82
|
||||
78 77 75 81 79 77 75 81
|
||||
80 77 75 81 81 83 85 87
|
||||
81 83 85 91 81 83 85 86
|
||||
82 81 83 84 82 81 83 85
|
||||
83 85 87 88 83 85 87 89
|
||||
83 85 87 90 83 85 91 96
|
||||
83 85 91 92 84 83 85 87
|
||||
84 83 85 91 84 83 85 86
|
||||
85 91 96 97 85 91 96 98
|
||||
86 85 87 88 86 85 87 89
|
||||
86 85 87 90 86 85 91 96
|
||||
86 85 91 92 87 85 91 96
|
||||
87 85 91 92 88 87 85 91
|
||||
89 87 85 91 90 87 85 91
|
||||
91 96 98 100 91 96 98 93
|
||||
91 96 98 99 92 91 96 97
|
||||
92 91 96 98 93 98 100 101
|
||||
93 98 100 102 93 98 100 103
|
||||
93 98 96 97 94 93 98 100
|
||||
94 93 98 96 94 93 98 99
|
||||
95 93 98 100 95 93 98 96
|
||||
95 93 98 99 96 98 100 101
|
||||
96 98 100 102 96 98 100 103
|
||||
97 96 98 100 97 96 98 99
|
||||
99 98 100 101 99 98 100 102
|
||||
99 98 100 103
|
||||
|
||||
19 !NIMPHI: impropers
|
||||
11 5 13 12 13 11 15 14
|
||||
21 15 23 22 23 21 25 24
|
||||
31 25 33 32 33 31 35 34
|
||||
41 35 43 42 43 41 45 44
|
||||
51 45 53 52 53 51 55 54
|
||||
61 55 63 62 63 61 65 64
|
||||
71 65 73 72 73 71 75 74
|
||||
81 75 83 82 83 81 85 84
|
||||
91 85 96 92 93 98 95 94
|
||||
96 91 98 97
|
||||
|
||||
0 !NDON: donors
|
||||
|
||||
|
||||
0 !NACC: acceptors
|
||||
|
||||
|
||||
0 !NNB
|
||||
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0
|
||||
|
||||
1 0 !NGRP
|
||||
0 0 0
|
||||
|
||||
16
examples/USER-MISC/imd/deca-ala_imd-demo.vmd
Normal file
16
examples/USER-MISC/imd/deca-ala_imd-demo.vmd
Normal file
@ -0,0 +1,16 @@
|
||||
#!/usr/local/bin/vmd
|
||||
# Display settings
|
||||
display projection Orthographic
|
||||
|
||||
mol new deca-ala.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
mol delrep 0 top
|
||||
mol representation Licorice
|
||||
mol color Name
|
||||
mol selection {all}
|
||||
mol material Glossy
|
||||
mol addrep top
|
||||
|
||||
imd connect localhost 5678
|
||||
sleep 1
|
||||
display resetview
|
||||
mouse mode forceres
|
||||
10
examples/USER-MISC/imd/falcon.tcl
Normal file
10
examples/USER-MISC/imd/falcon.tcl
Normal file
@ -0,0 +1,10 @@
|
||||
#!/usr/local/bin/vmd
|
||||
menu tool on
|
||||
tool create tug falcon0 fbuttons0 ffeedback0
|
||||
tool scale 50.0 0
|
||||
# tool scaleforce 50.0 0
|
||||
# tool scalespring 35.0
|
||||
tool scaleforce 15.0 0
|
||||
tool scalespring 15.0
|
||||
tool rep 0 -1 -1
|
||||
|
||||
59
examples/USER-MISC/imd/in.bucky-plus-cnt
Normal file
59
examples/USER-MISC/imd/in.bucky-plus-cnt
Normal file
@ -0,0 +1,59 @@
|
||||
# stick a buckyball into a nanotube
|
||||
units real
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style molecular
|
||||
newton on off
|
||||
|
||||
processors * * 1
|
||||
|
||||
# read topology
|
||||
read_data data.bucky-plus-cnt
|
||||
|
||||
pair_style lj/cut 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.0
|
||||
|
||||
pair_coeff 1 1 0.07 3.55
|
||||
pair_coeff 1 2 0.07 3.55
|
||||
pair_coeff 2 2 0.07 3.55
|
||||
bond_coeff 1 305.0 1.4
|
||||
angle_coeff 1 40.000 120.00 35.00 2.41620
|
||||
dihedral_coeff 1 3.100 2 180 0.0
|
||||
|
||||
neighbor 4.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
timestep 2.0
|
||||
|
||||
# we only move some atoms.
|
||||
group mobile type 1
|
||||
|
||||
# have balls bounce off the walls
|
||||
fix walls mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
|
||||
|
||||
velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
|
||||
|
||||
# take some potential energy out of the system
|
||||
minimize 1.0e-4 1.0e-6 100 1000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
fix integrate mobile nve
|
||||
fix thermostat mobile langevin 300.0 300.0 2000.0 234624
|
||||
|
||||
# IMD setup.
|
||||
fix comm all imd 6789 unwrap on trate 10
|
||||
#fix comm all imd 6789 unwrap on trate 10 nowait on
|
||||
|
||||
# temperature is based on mobile atoms only
|
||||
compute mobtemp mobile temp
|
||||
thermo_style custom step pe ke evdwl emol c_mobtemp spcpu
|
||||
thermo 1000
|
||||
thermo_modify norm yes
|
||||
thermo_modify temp mobtemp
|
||||
|
||||
run 100000000
|
||||
62
examples/USER-MISC/imd/in.bucky-plus-cnt-gpu
Normal file
62
examples/USER-MISC/imd/in.bucky-plus-cnt-gpu
Normal file
@ -0,0 +1,62 @@
|
||||
# stick a buckyball into a nanotube
|
||||
units real
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style molecular
|
||||
newton off
|
||||
|
||||
processors * * 1
|
||||
|
||||
# read topology
|
||||
read_data data.bucky-plus-cnt
|
||||
|
||||
pair_style lj/cut/gpu 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.0
|
||||
|
||||
pair_coeff 1 1 0.07 3.55
|
||||
pair_coeff 1 2 0.07 3.55
|
||||
pair_coeff 2 2 0.07 3.55
|
||||
bond_coeff 1 305.0 1.4
|
||||
angle_coeff 1 40.000 120.00 35.00 2.41620
|
||||
dihedral_coeff 1 3.100 2 180 0.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
timestep 2.0
|
||||
|
||||
# required for GPU acceleration
|
||||
fix gpu all gpu force 0 0 1.0
|
||||
|
||||
# we only move some atoms.
|
||||
group mobile type 1
|
||||
|
||||
# have balls bounce off the walls
|
||||
fix walls mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
|
||||
|
||||
velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
|
||||
|
||||
# take some potential energy out of the system
|
||||
minimize 1.0e-4 1.0e-6 100 1000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
fix integrate mobile nve
|
||||
fix thermostat mobile langevin 300.0 300.0 2000.0 234624
|
||||
|
||||
# IMD setup.
|
||||
fix comm all imd 6789 unwrap on trate 10
|
||||
#fix comm all imd 6789 unwrap on trate 10 nowait on
|
||||
|
||||
# temperature is based on mobile atoms only
|
||||
compute mobtemp mobile temp
|
||||
thermo_style custom step pe ke evdwl emol c_mobtemp spcpu
|
||||
thermo 1000
|
||||
thermo_modify norm yes
|
||||
thermo_modify temp mobtemp
|
||||
|
||||
run 100000000
|
||||
33
examples/USER-MISC/imd/in.deca-ala-solv-filter_imd
Normal file
33
examples/USER-MISC/imd/in.deca-ala-solv-filter_imd
Normal file
@ -0,0 +1,33 @@
|
||||
#
|
||||
units real
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 1 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 8 10
|
||||
pair_modify mix arithmetic
|
||||
special_bonds charmm
|
||||
read_data data.deca-ala-solv
|
||||
|
||||
|
||||
group peptide id <= 103
|
||||
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
kspace_style pppm 1e-5
|
||||
|
||||
fix ensemble all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 0.2
|
||||
|
||||
# IMD setup.
|
||||
fix comm all imd 5678 unwrap on trate 10 filter 20 2
|
||||
|
||||
run 5000000
|
||||
|
||||
|
||||
33
examples/USER-MISC/imd/in.deca-ala-solv_imd
Normal file
33
examples/USER-MISC/imd/in.deca-ala-solv_imd
Normal file
@ -0,0 +1,33 @@
|
||||
#
|
||||
units real
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 1 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 8 10
|
||||
pair_modify mix arithmetic
|
||||
special_bonds charmm
|
||||
read_data data.deca-ala-solv
|
||||
|
||||
|
||||
group peptide id <= 103
|
||||
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
kspace_style pppm 1e-5
|
||||
|
||||
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
|
||||
|
||||
# IMD setup.
|
||||
fix comm all imd 5678 unwrap on trate 10
|
||||
|
||||
run 5000000
|
||||
|
||||
|
||||
33
examples/USER-MISC/imd/in.deca-ala_imd
Normal file
33
examples/USER-MISC/imd/in.deca-ala_imd
Normal file
@ -0,0 +1,33 @@
|
||||
#
|
||||
units real
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 1 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 8 10
|
||||
pair_modify mix arithmetic
|
||||
special_bonds charmm
|
||||
read_data data.deca-ala-solv
|
||||
|
||||
|
||||
group peptide id <= 103
|
||||
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
kspace_style pppm 1e-5
|
||||
|
||||
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
|
||||
|
||||
# IMD setup.
|
||||
fix comm peptide imd 5678 unwrap on trate 10
|
||||
|
||||
run 5000000
|
||||
|
||||
|
||||
35
examples/USER-MISC/imd/in.deca-ala_imd-gpu
Normal file
35
examples/USER-MISC/imd/in.deca-ala_imd-gpu
Normal file
@ -0,0 +1,35 @@
|
||||
#
|
||||
units real
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 1 every 1
|
||||
newton off
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long/gpu 8 10
|
||||
pair_modify mix arithmetic
|
||||
special_bonds charmm
|
||||
read_data data.deca-ala-solv
|
||||
|
||||
fix 0 all gpu force/neigh 0 0 1.0
|
||||
|
||||
group peptide id <= 103
|
||||
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
|
||||
|
||||
# IMD setup.
|
||||
fix comm peptide imd 5678 unwrap on trate 10
|
||||
|
||||
run 5000000
|
||||
|
||||
|
||||
28
examples/USER-MISC/imd/in.melt_imd
Normal file
28
examples/USER-MISC/imd/in.melt_imd
Normal file
@ -0,0 +1,28 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 5 delay 10 check yes
|
||||
|
||||
thermo_style custom step pe ke spcpu
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# IMD setup.
|
||||
fix comm all imd 5678 unwrap off fscale 20.0 trate 10 nowait on
|
||||
|
||||
thermo 500
|
||||
run 5000000
|
||||
30
examples/USER-MISC/imd/in.melt_imd-gpu
Normal file
30
examples/USER-MISC/imd/in.melt_imd-gpu
Normal file
@ -0,0 +1,30 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
newton off
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut/gpu 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 5 delay 10 check yes
|
||||
|
||||
thermo_style custom step pe ke spcpu
|
||||
|
||||
fix 0 all gpu force/neigh 0 0 1.0
|
||||
fix 1 all nve
|
||||
|
||||
# IMD setup.
|
||||
fix comm all imd 5678 unwrap off fscale 20.0 trate 20 nowait on
|
||||
|
||||
thermo 500
|
||||
run 5000000
|
||||
4532
examples/USER-MISC/imd/melt.psf
Normal file
4532
examples/USER-MISC/imd/melt.psf
Normal file
File diff suppressed because it is too large
Load Diff
18
examples/USER-MISC/imd/melt_imd-demo.vmd
Normal file
18
examples/USER-MISC/imd/melt_imd-demo.vmd
Normal file
@ -0,0 +1,18 @@
|
||||
#!/usr/local/bin/vmd
|
||||
# Display settings
|
||||
display projection Orthographic
|
||||
|
||||
mol new melt.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
mol delrep 0 top
|
||||
mol representation VDW 0.400000 8.000000
|
||||
mol color Name
|
||||
mol selection {all}
|
||||
mol material Glossy
|
||||
mol addrep top
|
||||
mol selection {index 0}
|
||||
mol color ColorID 0
|
||||
mol representation VDW 0.600000 8.000000
|
||||
mol addrep top
|
||||
|
||||
imd connect localhost 5678
|
||||
mouse mode forceatom
|
||||
Reference in New Issue
Block a user