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