Mercurial > repos > chemteam > gmx_sim
comparison sim.xml @ 15:ea0e6d2f1be7 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 15:27:11 +0000 |
| parents | 525ca7c8065f |
| children | 633f27174e8f |
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| 14:525ca7c8065f | 15:ea0e6d2f1be7 |
|---|---|
| 1 <tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | 1 <tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> |
| 2 <description>for system equilibration or data collection</description> | 2 <description>for system equilibration or data collection</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 <token name="@GALAXY_VERSION@">2</token> | 5 <token name="@GALAXY_VERSION@">3</token> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 #if $sets.mdp.mdpfile == "custom": | 9 #if $sets.mdp.mdpfile == "custom": |
| 10 ln -s '$sets.mdp.mdp_input' ./md.mdp && | 10 ln -s '$sets.mdp.mdp_input' ./md.mdp && |
| 96 ; Electrostatics | 96 ; Electrostatics |
| 97 coulombtype = $sets.mdp.coulombtype ; method for electrostatics calculations e.g. PME | 97 coulombtype = $sets.mdp.coulombtype ; method for electrostatics calculations e.g. PME |
| 98 pme_order = 4 ; cubic interpolation | 98 pme_order = 4 ; cubic interpolation |
| 99 fourierspacing = 0.16 ; grid spacing for FFT | 99 fourierspacing = 0.16 ; grid spacing for FFT |
| 100 ; Temperature coupling is on | 100 ; Temperature coupling is on |
| 101 tcoupl = V-rescale ; modified Berendsen thermostat | 101 tcoupl = V-rescale ; modified Berendsen thermostat |
| 102 tc-grps = Protein Non-Protein ; two coupling groups - more accurate | 102 #if $sets.mdp.systemTcouple == "true": |
| 103 tc-grps = System ; coupling the whole system. Can be used in any system, beyond peptides. | |
| 104 tau_t = 0.1 ; time constant in ps | |
| 105 ref_t = $sets.mdp.temperature | |
| 106 #else | |
| 107 tc-grps = Protein Non-Protein ; two coupling groups - more accurate | |
| 103 tau_t = 0.1 0.1 ; time constant, in ps | 108 tau_t = 0.1 0.1 ; time constant, in ps |
| 104 ref_t = $sets.mdp.temperature $sets.mdp.temperature ; reference temperature, one for each group, in K | 109 ref_t = $sets.mdp.temperature $sets.mdp.temperature ; reference temperature, one for each group, in K |
| 110 #end if | |
| 105 ; Periodic boundary conditions | 111 ; Periodic boundary conditions |
| 106 pbc = xyz ; 3-D PBC | 112 pbc = xyz ; 3-D PBC |
| 107 ; Dispersion correction | 113 ; Dispersion correction |
| 108 DispCorr = EnerPres ; account for cut-off vdW scheme | 114 DispCorr = EnerPres ; account for cut-off vdW scheme |
| 109 ; Velocity generation | 115 ; Velocity generation |
| 110 gen_vel = no ; Velocity generation is off | 116 #if $sets.ensembleselect.ensemble == "npt" or $sets.ensembleselect.startvel == "false": |
| 117 gen_vel = no ; Velocity generation is OFF | |
| 118 #else | |
| 119 gen_vel = yes ; Velocity generation is ON | |
| 120 #end if | |
| 111 #end if | 121 #end if |
| 112 #if $inps.itp_in: | 122 #if $inps.itp_in: |
| 113 define = -DPOSRES ; position restrain the protein | 123 define = -DPOSRES ; position restrain the protein |
| 114 refcoord_scaling = com | 124 refcoord_scaling = com |
| 115 #end if | 125 #end if |
| 116 #if $sets.ensemble == "nvt": | 126 #if $sets.ensembleselect.ensemble == "nvt": |
| 117 pcoupl = no ; no pressure coupling in NVT | 127 pcoupl = no ; no pressure coupling in NVT |
| 118 #else: | 128 #else: |
| 119 ; Pressure coupling is on | 129 ; Pressure coupling is on |
| 120 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT | 130 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT |
| 121 pcoupltype = isotropic ; uniform scaling of box vectors | 131 pcoupltype = isotropic ; uniform scaling of box vectors |
| 122 tau_p = 2.0 ; time constant, in ps | 132 tau_p = 2.0 ; time constant, in ps |
| 123 ref_p = 1.0 ; reference pressure, in bar | 133 ref_p = 1.0 ; reference pressure, in bar |
| 128 | 138 |
| 129 </configfiles> | 139 </configfiles> |
| 130 <inputs> | 140 <inputs> |
| 131 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> | 141 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> |
| 132 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> | 142 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> |
| 133 | 143 |
| 134 <section name="inps" title="Inputs" expanded="false"> | 144 <section name="inps" title="Inputs" expanded="false"> |
| 135 | 145 |
| 136 <!-- CPT inp --> | 146 <!-- CPT inp --> |
| 137 <!-- <conditional name="cpt_inp"> | 147 <!-- <conditional name="cpt_inp"> |
| 138 <param name="cpt_bool" type="select" label="Use a checkpoint (CPT) file" help="CPT file from a previous MD run"> | 148 <param name="cpt_bool" type="select" label="Use a checkpoint (CPT) file" help="CPT file from a previous MD run"> |
| 172 </when> | 182 </when> |
| 173 <when value="false"/> | 183 <when value="false"/> |
| 174 </conditional> --> | 184 </conditional> --> |
| 175 | 185 |
| 176 <param argument="ndx_in" type="data" format='ndx' label="Index (ndx) file" optional="true" help="Use an index file specifying custom atom groups. Leave empty to use default generated group"/> | 186 <param argument="ndx_in" type="data" format='ndx' label="Index (ndx) file" optional="true" help="Use an index file specifying custom atom groups. Leave empty to use default generated group"/> |
| 187 | |
| 177 | 188 |
| 178 </section> | 189 </section> |
| 179 | 190 |
| 180 <section name="outps" title="Outputs" expanded="false"> | 191 <section name="outps" title="Outputs" expanded="false"> |
| 181 <!-- TRAJ out --> | 192 <!-- TRAJ out --> |
| 220 | 231 |
| 221 </section> | 232 </section> |
| 222 | 233 |
| 223 <section name="sets" title="Settings" expanded="false"> | 234 <section name="sets" title="Settings" expanded="false"> |
| 224 <!-- other ... --> | 235 <!-- other ... --> |
| 225 <param name="ensemble" label="Ensemble" type="select" help="NVT ensemble (constant number of particles, volume and temperature) or NPT ensemble (constant number of particles, pressure and temperature)"> | 236 |
| 237 <conditional name="ensembleselect"> | |
| 238 <param name="ensemble" label="Ensemble" type="select" help="NVT ensemble (constant number of particles, volume and temperature) or NPT ensemble (constant number of particles, pressure and temperature)"> | |
| 226 <option value="nvt">Isothermal-isochoric ensemble (NVT)</option> | 239 <option value="nvt">Isothermal-isochoric ensemble (NVT)</option> |
| 227 <option value="npt">Isothermal-isobaric ensemble (NPT)</option> | 240 <option value="npt">Isothermal-isobaric ensemble (NPT)</option> |
| 228 </param> | 241 </param> |
| 229 | 242 <when value="nvt"> |
| 230 <expand macro="md_inputs"/> | 243 <param argument="startvel" type="select" label="Starting Velocities"> |
| 244 <option value="true">Assign starting velocities (recommended for NVT)</option> | |
| 245 <option value="false" selected="true">Do not assign starting velocities</option> | |
| 246 </param> | |
| 247 </when> | |
| 248 <when value="npt" /> | |
| 249 </conditional> | |
| 250 <expand macro="md_inputs"/> | |
| 231 </section> | 251 </section> |
| 232 | 252 |
| 233 <expand macro="maxwarn" /> | 253 <expand macro="maxwarn" /> |
| 234 <expand macro="log" /> | 254 <expand macro="log" /> |
| 235 | 255 |