Mercurial > repos > chemteam > gmx_trj
annotate macros.xml @ 1:e9cc595562b8 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
| author | chemteam |
|---|---|
| date | Thu, 13 Feb 2020 03:51:40 -0500 |
| parents | bb0053c4e4f2 |
| children | 6ac5f450ad31 |
| rev | line source |
|---|---|
|
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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1 <macros> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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2 <token name="@VERSION@">2019.1.4</token> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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3 <xml name="requirements"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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4 <requirements> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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5 <requirement type="package" version="2019.1">gromacs</requirement> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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6 </requirements> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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7 </xml> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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8 <xml name="citations"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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9 <citations> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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10 <citation type="doi">10.1016/j.softx.2015.06.001</citation> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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11 </citations> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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12 </xml> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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13 <xml name="md_inputs"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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14 |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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15 <conditional name="mdp"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
diff
changeset
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16 <param name="mdpfile" type="select" label="Parameter input"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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17 <option value="custom">Upload own MDP file</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
diff
changeset
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18 <option value="default">Use default (partially customisable) setting</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
diff
changeset
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19 </param> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
diff
changeset
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20 <when value="custom"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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21 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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22 </when> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
diff
changeset
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23 <when value="default"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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24 <param argument="integrator" type="select" label="Choice of integrator"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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25 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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26 <option value="sd">Stochastic dynamics integrator</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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27 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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28 </param> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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29 <param argument="constraints" type="select" label="Bond constraints (constraints)"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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30 <option value="none">No constraints except for those defined explicitly in the topology (none).</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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31 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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32 <option value="all-bonds">All bonds (all-bonds).</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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33 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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changeset
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34 <option value="all-angles">All bonds and angles (all-angles).</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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35 </param> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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36 <param argument="cutoffscheme" type="select" label="Neighbor searching"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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37 <option value="Verlet">Generate a pair list with buffering.</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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38 <option value="group">Generate a pair list for groups of atoms.</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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39 </param> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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40 <param argument="coulombtype" type="select" label="Electrostatics"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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41 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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42 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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43 <option value="Reaction-Field-zero">Reaction field electrostatics.</option> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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44 </param> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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45 |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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46 <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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47 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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48 <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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49 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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50 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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51 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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52 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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53 |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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54 </when> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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55 |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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56 </conditional> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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57 |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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58 </xml> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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59 |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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60 <xml name="log"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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61 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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62 </xml> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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63 |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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64 <xml name="log_outputs"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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65 <data name="report" format="txt" from_work_dir="verbose.txt"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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66 <filter>capture_log</filter> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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67 </data> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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68 </xml> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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69 |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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70 <xml name="test_params"> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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71 <param name="mdpfile" value="default" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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72 <param name="step_length" value="0.002"/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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73 <param name="md_steps" value="500"/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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74 <param name="write_freq" value="50"/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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75 <param name="temperature" value="300"/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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76 <param name="integrator" value="md" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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77 <param name="constraints" value="all-bonds"/> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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78 <param name="cutoffscheme" value="Verlet" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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79 <param name="coulombtype" value="PME" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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80 <param name="rlist" value="1.0" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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81 <param name="rcoulomb" value="1.0" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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82 <param name="rvdw" value="1.0" /> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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83 </xml> |
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bb0053c4e4f2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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84 </macros> |