Mercurial > repos > chemteam > gmx_restraints
annotate macros.xml @ 8:14a7bf3e03df draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
| author | chemteam |
|---|---|
| date | Wed, 29 Sep 2021 07:41:24 +0000 |
| parents | 642ce5c16ae8 |
| children | 54eadeb47ab9 |
| rev | line source |
|---|---|
|
0
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
1 <macros> |
|
8
14a7bf3e03df
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
chemteam
parents:
7
diff
changeset
|
2 <token name="@TOOL_VERSION@">2021.3</token> |
|
0
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
3 <xml name="requirements"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
4 <requirements> |
|
6
ca6a4740114e
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
5
diff
changeset
|
5 <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> |
|
0
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
6 </requirements> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
7 </xml> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
8 <xml name="citations"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
9 <citations> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
10 <citation type="doi">10.1016/j.softx.2015.06.001</citation> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
11 </citations> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
12 </xml> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
13 <xml name="md_inputs"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
14 |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
15 <conditional name="mdp"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
16 <param name="mdpfile" type="select" label="Parameter input"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
17 <option value="custom">Upload own MDP file</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
18 <option value="default">Use default (partially customisable) setting</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
19 </param> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
20 <when value="custom"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
21 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
22 </when> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
23 <when value="default"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
24 <param argument="integrator" type="select" label="Choice of integrator"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
25 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
26 <option value="sd">Stochastic dynamics integrator</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
27 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
28 </param> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
29 <param argument="constraints" type="select" label="Bond constraints (constraints)"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
30 <option value="none">No constraints except for those defined explicitly in the topology (none).</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
31 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
32 <option value="all-bonds">All bonds (all-bonds).</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
33 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
34 <option value="all-angles">All bonds and angles (all-angles).</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
35 </param> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
36 <param argument="cutoffscheme" type="select" label="Neighbor searching"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
37 <option value="Verlet">Generate a pair list with buffering.</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
38 <option value="group">Generate a pair list for groups of atoms.</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
39 </param> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
40 <param argument="coulombtype" type="select" label="Electrostatics"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
41 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
42 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
43 <option value="Reaction-Field-zero">Reaction field electrostatics.</option> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
44 </param> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
45 |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
46 <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
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." /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
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." /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
49 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
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."/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
51 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
52 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
53 |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
54 </when> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
55 |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
56 </conditional> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
57 |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
58 </xml> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
59 |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
60 <xml name="log"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
61 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
62 </xml> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
63 |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
64 <xml name="log_outputs"> |
|
8
14a7bf3e03df
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
chemteam
parents:
7
diff
changeset
|
65 <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}"> |
|
0
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
66 <filter>capture_log</filter> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
67 </data> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
68 </xml> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
69 |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
70 <xml name="test_params"> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
71 <param name="mdpfile" value="default" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
72 <param name="step_length" value="0.002"/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
73 <param name="md_steps" value="500"/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
74 <param name="write_freq" value="50"/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
75 <param name="temperature" value="300"/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
76 <param name="integrator" value="md" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
77 <param name="constraints" value="all-bonds"/> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
78 <param name="cutoffscheme" value="Verlet" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
79 <param name="coulombtype" value="PME" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
80 <param name="rlist" value="1.0" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
81 <param name="rcoulomb" value="1.0" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
82 <param name="rvdw" value="1.0" /> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
83 </xml> |
|
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
|
84 </macros> |