Mercurial > repos > chemteam > gmx_merge_topology_files
comparison test-data/oplsaa.ff-tip4p.itp @ 16:3cf3b3b305ea draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
| author | chemteam |
|---|---|
| date | Tue, 21 Dec 2021 13:41:56 +0000 |
| parents | |
| children |
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| 15:3c56532ba462 | 16:3cf3b3b305ea |
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| 1 ; | |
| 2 ; Note the strange order of atoms to make it faster in gromacs. | |
| 3 ; | |
| 4 [ moleculetype ] | |
| 5 ; molname nrexcl | |
| 6 SOL 2 | |
| 7 | |
| 8 [ atoms ] | |
| 9 ; id at type res nr residu name at name cg nr charge | |
| 10 1 opls_113 1 SOL OW 1 0.0 | |
| 11 2 opls_114 1 SOL HW1 1 0.52 | |
| 12 3 opls_114 1 SOL HW2 1 0.52 | |
| 13 4 opls_115 1 SOL MW 1 -1.04 | |
| 14 | |
| 15 #ifndef FLEXIBLE | |
| 16 [ settles ] | |
| 17 ; OW funct doh dhh | |
| 18 1 1 0.09572 0.15139 | |
| 19 #else | |
| 20 [ bonds ] | |
| 21 ; i j funct length force.c. | |
| 22 1 2 1 0.09572 502416.0 0.09572 502416.0 | |
| 23 1 3 1 0.09572 502416.0 0.09572 502416.0 | |
| 24 | |
| 25 [ angles ] | |
| 26 ; i j k funct angle force.c. | |
| 27 2 1 3 1 104.52 628.02 104.52 628.02 | |
| 28 #endif | |
| 29 | |
| 30 [ exclusions ] | |
| 31 1 2 3 4 | |
| 32 2 1 3 4 | |
| 33 3 1 2 4 | |
| 34 4 1 2 3 | |
| 35 | |
| 36 ; The position of the virtual site is computed as follows: | |
| 37 ; | |
| 38 ; O | |
| 39 ; | |
| 40 ; D | |
| 41 ; | |
| 42 ; H H | |
| 43 ; | |
| 44 ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ] | |
| 45 ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ] | |
| 46 | |
| 47 ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) | |
| 48 | |
| 49 [ virtual_sites3 ] | |
| 50 ; Vsite from funct a b | |
| 51 4 1 2 3 1 0.128012065 0.128012065 | |
| 52 |