Mercurial > repos > chemteam > gmx_energy
changeset 10:dae135dfd519 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0"
| author | chemteam |
|---|---|
| date | Tue, 30 Nov 2021 15:30:43 +0000 |
| parents | 97872d87ba80 |
| children | 58c3e6711e94 |
| files | macros.xml |
| diffstat | 1 files changed, 7 insertions(+), 4 deletions(-) [+] |
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--- a/macros.xml Wed Oct 27 08:01:58 2021 +0000 +++ b/macros.xml Tue Nov 30 15:30:43 2021 +0000 @@ -5,7 +5,6 @@ <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> </requirements> </xml> - <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token> <xml name="citations"> @@ -45,14 +44,17 @@ <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> <option value="Reaction-Field-zero">Reaction field electrostatics.</option> </param> - - <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" /> + <param name="temperature" type="integer" label="Temperature (K)" value="0" min="0" max="1000000" help="Temperature" /> + <param name="systemTcouple" type="select" label="Number of groups to set for thermocoupling"> + <option value="true">Single coupling group (System)</option> + <option value="false" selected="true">Two coupling groups (Protein and Non-Protein)</option> + </param> <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> <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." /> <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> <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."/> <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> - <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" /> + <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" help="MD steps" /> </when> @@ -68,6 +70,7 @@ <param name="mxw" value="0" min="0" argument="-maxwarn" type="integer" label="Maximum warnings to allow." help="Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail."/> </xml> + <xml name="log_outputs"> <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}"> <filter>capture_log</filter>