Mercurial > repos > chemteam > gmx_sim

changeset 15:ea0e6d2f1be7 draft

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"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 ef8e6d99fc15
files macros.xml sim.xml
diffstat 2 files changed, 38 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Oct 27 08:02:22 2021 +0000
+++ b/macros.xml	Tue Nov 30 15:27:11 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>
--- a/sim.xml	Wed Oct 27 08:02:22 2021 +0000
+++ b/sim.xml	Tue Nov 30 15:27:11 2021 +0000
@@ -2,7 +2,7 @@
     <description>for system equilibration or data collection</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">3</token>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
@@ -98,24 +98,34 @@
                     pme_order      = 4        ; cubic interpolation
                     fourierspacing  = 0.16    ; grid spacing for FFT
                     ; Temperature coupling is on
-                    tcoupl    = V-rescale              ; modified Berendsen thermostat
-                    tc-grps    = Protein Non-Protein  ; two coupling groups - more accurate
+                    tcoupl   = V-rescale ; modified Berendsen thermostat
+                    #if $sets.mdp.systemTcouple == "true":
+                    tc-grps = System ; coupling the whole system. Can be used in any system, beyond peptides.
+                    tau_t    = 0.1 ; time constant in ps
+                    ref_t    = $sets.mdp.temperature
+                    #else
+                    tc-grps   = Protein Non-Protein  ; two coupling groups - more accurate
                     tau_t    = 0.1    0.1          ; time constant, in ps
                     ref_t    = $sets.mdp.temperature $sets.mdp.temperature           ; reference temperature, one for each group, in K
+                    #end if
                     ; Periodic boundary conditions
                     pbc    = xyz    ; 3-D PBC
                     ; Dispersion correction
                     DispCorr  = EnerPres  ; account for cut-off vdW scheme
                     ; Velocity generation
-                    gen_vel    = no    ; Velocity generation is off
+                    #if $sets.ensembleselect.ensemble == "npt" or $sets.ensembleselect.startvel == "false":
+                    gen_vel    = no    ; Velocity generation is OFF
+                    #else
+                    gen_vel    = yes    ; Velocity generation is ON
+                    #end if
                 #end if
                 #if $inps.itp_in:
                     define    = -DPOSRES  ; position restrain the protein
                     refcoord_scaling  = com
                 #end if
-                #if $sets.ensemble == "nvt":
+                #if $sets.ensembleselect.ensemble == "nvt":
                     pcoupl    = no     ; no pressure coupling in NVT
-                #else: 
+                #else:
                     ; Pressure coupling is on
                     pcoupl            = Parrinello-Rahman      ; Pressure coupling on in NPT
                     pcoupltype          = isotropic              ; uniform scaling of box vectors
@@ -130,7 +140,7 @@
     <inputs>
         <param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
         <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
-
+ 
         <section name="inps" title="Inputs" expanded="false">
         
             <!-- CPT inp -->
@@ -174,6 +184,7 @@
             </conditional> -->
 
             <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"/>
+            
 
         </section>
 
@@ -222,12 +233,21 @@
 
         <section name="sets" title="Settings" expanded="false">
             <!-- other ... -->
-            <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)">
+            
+            <conditional name="ensembleselect">
+              <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)">
                 <option value="nvt">Isothermal-isochoric ensemble (NVT)</option>
                 <option value="npt">Isothermal-isobaric ensemble (NPT)</option>
-            </param>
-
-            <expand macro="md_inputs"/>
+              </param>
+                  <when value="nvt">
+                     <param argument="startvel" type="select" label="Starting Velocities">
+                        <option value="true">Assign starting velocities (recommended for NVT)</option>
+                        <option value="false" selected="true">Do not assign starting velocities</option>
+                     </param>
+                  </when>
+                  <when value="npt" />
+            </conditional>            
+          <expand macro="md_inputs"/>
         </section>
         
         <expand macro="maxwarn" />