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comparison minim.xml @ 0:c581846ec2cb draft

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author fmercuri
date Mon, 28 Jun 2021 08:57:49 +0000
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1 <tool id="gmx_em" name="GROMACS energy minimization daimoners' version" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>of the system prior to equilibration and production MD</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7
8 <expand macro="requirements" />
9
10 <command detect_errors="exit_code"><![CDATA[
11
12 #if $mdp.mdpfile == 'custom':
13 ln -s '$mdp.mdp_input' ./minim.mdp &&
14 #else:
15 ln -s '$minim' ./minim.mdp &&
16 #end if
17
18 ln -s '$gro_input' ./solv_ions.gro &&
19 ln -s '$top_input' ./top_input.top &&
20
21 gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr -maxwarn 5 &>> verbose.txt &&
22 gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm em &>> verbose.txt
23
24 ]]></command>
25 <configfiles>
26 <!-- .mdp files for the gromacs simulation -->
27 <configfile name="minim">
28 #if $mdp.mdpfile == 'default':
29 ; minim.mdp - used as input into grompp to generate em.tpr
30 integrator = $mdp.integrator ; Algorithm (steep = steepest descent minimization)
31 emtol = $mdp.emtol ; Stop minimization when the maximum force is less than this value
32 emstep = $mdp.emstep ; Energy step size
33 nsteps = $mdp.md_steps ; Maximum number of (minimization) steps to perform
34
35 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
36 nstlist = 1 ; Frequency to update the neighbor list and long range forces
37 cutoff-scheme = $mdp.cutoffscheme
38 ns_type = grid ; Method to determine neighbor list (simple, grid)
39 coulombtype = $mdp.coulombtype ; Treatment of long range electrostatic interactions
40 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
41 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
42 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
43 pbc = xyz ; Periodic Boundary Conditions (yes/no)
44 #end if
45 </configfile>
46 </configfiles>
47
48 <inputs>
49 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
50 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
51 <conditional name="mdp">
52 <param name="mdpfile" type="select" label="Parameter input">
53 <option value="custom">Upload own MDP file</option>
54 <option value="default">Use default (partially customisable) setting</option>
55 </param>
56 <when value="custom">
57 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/>
58 </when>
59
60 <when value="default">
61 <param argument="integrator" type="select" label="Choice of integrator.">
62 <option value="steep">Steepest descent algorithm.</option>
63 <option value="cg">Conjugate gradient algorithm.</option>
64 <option value="l-bfgs">Quasi-Newtonian algorithm.</option>
65 </param>
66 <param argument="cutoffscheme" type="select" label="Neighbor searching.">
67 <option value="Verlet">Generate a pair list with buffering.</option>
68 <option value="group">Generate a pair list for groups of atoms.</option>
69 </param>
70 <param argument="coulombtype" type="select" label="Electrostatics.">
71 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
72 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
73 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
74 </param>
75 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
76 <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."/>
77 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
78 <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" />
79 <param argument="emtol" type="float" label="EM tolerance" value="0" min="0" max="10000" help="The minimization is converged when the maximum force is smaller than this value" />
80 <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." />
81 </when>
82 </conditional>
83 <expand macro="log" />
84 </inputs>
85 <outputs>
86 <data name="output1" format="gro" from_work_dir="em.gro"/>
87 <data name="output2" format="edr" from_work_dir="em.edr"/>
88 <expand macro="log_outputs" />
89 </outputs>
90 <tests>
91 <test>
92 <param name="gro_input" value="str_ions.gro" />
93 <param name="top_input" value="topol_solv.top" />
94 <param name="mdpfile" value="default" />
95 <param name="integrator" value="steep" />
96 <param name="cutoffscheme" value="Verlet" />
97 <param name="coulombtype" value="PME" />
98 <param name="rcoulomb" value="1.0" />
99 <param name="rlist" value="1.0" />
100 <param name="md_steps" value="50000" />
101 <param name="emtol" value="1000.0" />
102 <param name="emstep" value="0.01" />
103 <output name="output1" ftype="gro" >
104 <assert_contents>
105 <has_size value="4281" />
106 </assert_contents>
107 </output>
108 <output name="output2" ftype="edr" >
109 <assert_contents>
110 <!-- this binary can vary in size a lot unfortunately -->
111 <has_size value="5000" delta="1000" />
112 </assert_contents>
113 </output>
114 </test>
115 <test>
116 <param name="gro_input" value="str_ions.gro" />
117 <param name="top_input" value="topol_solv.top" />
118 <param name="mdpfile" value="custom" />
119 <param name="mdp_input" value="minim.mdp" />
120 <output name="output1" ftype="gro" >
121 <assert_contents>
122 <has_size value="4281" />
123 </assert_contents>
124 </output>
125 <output name="output2" ftype="edr" >
126 <assert_contents>
127 <!-- this binary can vary in size a lot unfortunately -->
128 <has_size value="5000" delta="1000" />
129 </assert_contents>
130 </output>
131 </test>
132
133 </tests>
134 <help><![CDATA[
135
136 .. class:: infomark
137
138 **What it does**
139
140 This tool performs energy minimization of a system prior to a GROMACS simulation.
141
142 _____
143
144 .. class:: infomark
145
146 **Input**
147
148 - GRO structure file.
149 - Topology (TOP) file.
150 - MDP parameter file (optional)
151
152 To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options.
153
154 .. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
155
156 _____
157
158
159 .. class:: infomark
160
161 **Output**
162
163 - GRO structure file.
164
165 ]]></help>
166
167 <expand macro="citations" />
168 </tool>