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annotate test-data/oplsaa.ff-tip4p.itp @ 1:e8e3636338c8 draft default tip

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
author chemteam
date Mon, 24 Oct 2022 22:31:09 +0000
parents 7f64dd60f5d7
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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1 ;
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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2 ; Note the strange order of atoms to make it faster in gromacs.
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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3 ;
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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4 [ moleculetype ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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5 ; molname nrexcl
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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6 SOL 2
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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8 [ atoms ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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9 ; id at type res nr residu name at name cg nr charge
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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10 1 opls_113 1 SOL OW 1 0.0
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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11 2 opls_114 1 SOL HW1 1 0.52
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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12 3 opls_114 1 SOL HW2 1 0.52
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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13 4 opls_115 1 SOL MW 1 -1.04
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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15 #ifndef FLEXIBLE
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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16 [ settles ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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17 ; OW funct doh dhh
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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18 1 1 0.09572 0.15139
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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19 #else
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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20 [ bonds ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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21 ; i j funct length force.c.
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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22 1 2 1 0.09572 502416.0 0.09572 502416.0
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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23 1 3 1 0.09572 502416.0 0.09572 502416.0
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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25 [ angles ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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26 ; i j k funct angle force.c.
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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27 2 1 3 1 104.52 628.02 104.52 628.02
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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28 #endif
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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30 [ exclusions ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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31 1 2 3 4
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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32 2 1 3 4
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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33 3 1 2 4
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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34 4 1 2 3
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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35
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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36 ; The position of the virtual site is computed as follows:
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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37 ;
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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38 ; O
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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39 ;
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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40 ; D
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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41 ;
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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42 ; H H
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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43 ;
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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44 ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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45 ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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46
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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47 ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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48
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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49 [ virtual_sites3 ]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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50 ; Vsite from funct a b
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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51 4 1 2 3 1 0.128012065 0.128012065
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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52