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comparison nvt.xml @ 0:666dc804011d draft

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author fmercuri
date Mon, 28 Jun 2021 10:08:59 +0000
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1 <tool id="gmx_nvt" name="GROMACS NVT equilibration" version="@VERSION@">
2 <description>- constant-temperature and -volume equilibration of a system</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements" />
8
9 <command detect_errors="exit_code"><![CDATA[
10 #if $mdp.mdpfile == "custom":
11 ln -s '$mdp.mdp_input' ./nvt.mdp &&
12 #end if
13 #if $mdp.mdpfile == "default":
14 ln -s '$nvt' ./nvt.mdp &&
15 #end if
16
17 ln -s '$gro_input' ./em.gro &&
18 ln -s '$top_input' ./top_input.top &&
19 ln -s '$itp_input' ./posres.itp &&
20
21 gmx grompp -f ./nvt.mdp -c ./em.gro -r ./em.gro -p ./top_input.top -o nvt.tpr &>> verbose.txt &&
22 gmx mdrun -deffnm nvt &>> verbose.txt
23
24 #if $str == 'pdb' or $str == 'both'
25 && gmx editconf -f nvt.gro -o nvt.pdb &>> verbose.txt
26 #end if
27 ]]></command>
28 <configfiles>
29 <!-- .mdp file for the gromacs simulation -->
30 <configfile name="nvt">
31 #if $mdp.mdpfile == 'default':
32 title = NVT equilibration
33 define = -DPOSRES ; position restrain the protein
34 ; Run parameters
35 integrator = $mdp.integrator ; leap-frog integrator
36 nsteps = $mdp.md_steps ; 2 * 50000 = 100 ps
37 dt = $mdp.step_length ; 2 fs
38 ; Output control
39 nstxout = $mdp.write_freq ; save coordinates every n ps
40 nstvout = $mdp.write_freq ; save velocities every n ps
41 nstenergy = $mdp.write_freq ; save energies every n ps
42 nstlog = $mdp.write_freq ; update log file every n ps
43 nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps
44 ; Bond parameters
45 continuation = no ; first dynamics run
46 constraint_algorithm = lincs ; holonomic constraints
47 constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained
48 lincs_iter = 1 ; accuracy of LINCS
49 lincs_order = 4 ; also related to accuracy
50 ; Neighborsearching
51 cutoff-scheme = $mdp.cutoffscheme
52 ns_type = grid ; search neighboring grid cells
53 nstlist = 10 ; 20 fs, largely irrelevant with Verlet
54 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
55 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
56 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
57 ; Electrostatics
58 coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME
59 pme_order = 4 ; cubic interpolation
60 fourierspacing = 0.16 ; grid spacing for FFT
61 ; Temperature coupling is on
62 tcoupl = V-rescale ; modified Berendsen thermostat
63 tc-grps = $mdp.sysname ; two coupling groups - more accurate
64 tau_t = 0.1 ; time constant, in ps
65 ref_t = $mdp.temperature; reference temperature, one for each group, in K
66 ; Pressure coupling is off
67 pcoupl = no ; no pressure coupling in NVT
68 ; Periodic boundary conditions
69 pbc = xyz ; 3-D PBC
70 ; Dispersion correction
71 DispCorr = EnerPres ; account for cut-off vdW scheme
72 ; Velocity generation
73 gen_vel = yes ; assign velocities from Maxwell distribution
74 gen_temp = 300 ; temperature for Maxwell distribution
75 gen_seed = -1 ; generate a random seed
76 #end if
77 </configfile>
78
79 </configfiles>
80 <inputs>
81 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
82 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
83 <param argument="itp_input" type="data" format='itp' label="Position restraint file."/>
84
85 <expand macro="md_inputs"/>
86 </inputs>
87 <outputs>
88 <data name="output1" format="gro" from_work_dir="nvt.gro">
89 <filter>str == 'gro' or str == 'both'</filter>
90 </data>
91 <data name="output5" format="pdb" from_work_dir="nvt.pdb">
92 <filter>str == 'pdb' or str == 'both'</filter>
93 </data>
94 <data name="output2" format="cpt" from_work_dir="nvt.cpt"/>
95 <data name="output3" format="trr" from_work_dir="nvt.trr">
96 <filter>traj == 'trr' or traj == 'both'</filter>
97 </data>
98 <data name="output4" format="xtc" from_work_dir="nvt.xtc">
99 <filter>traj == 'xtc' or traj == 'both'</filter>
100 </data>
101 <data name="report" format="txt" from_work_dir="verbose.txt">
102 <filter>capture_log</filter>
103 </data>
104 </outputs>
105 <tests>
106 <test>
107 <param name="gro_input" value="em.gro" />
108 <param name="top_input" value="topol_solv.top" />
109 <param name="itp_input" value="posres.itp" />
110 <param name="traj" value="xtc"/>
111 <param name="str" value="both"/>
112
113 <expand macro="test_params"/>
114
115 <output name="output1" file="nvt.gro" ftype="gro" compare="sim_size"/>
116 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
117 <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/>
118 <output name="output5" file="nvt.pdb" ftype="pdb" compare="sim_size"/>
119
120 </test>
121 <test>
122 <param name="gro_input" value="em.gro" />
123 <param name="top_input" value="topol_solv.top" />
124 <param name="itp_input" value="posres.itp" />
125 <param name="traj" value="xtc"/>
126 <param name="str" value="pdb"/>
127
128 <expand macro="test_params"/>
129
130 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
131 <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/>
132 <output name="output5" file="nvt.pdb" ftype="pdb" compare="sim_size"/>
133
134 </test>
135 <test>
136 <param name="gro_input" value="em.gro" />
137 <param name="top_input" value="topol_solv.top" />
138 <param name="itp_input" value="posres.itp" />
139 <param name="str" value="gro"/>
140 <param name="traj" value="trr"/>
141
142 <expand macro="test_params"/>
143
144 <output name="output1" file="nvt.gro" ftype="gro" compare="sim_size"/>
145 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
146 <output name="output3" file="nvt.trr" ftype="trr" compare="sim_size"/>
147 </test>
148 <test>
149 <param name="gro_input" value="em.gro" />
150 <param name="top_input" value="topol_solv.top" />
151 <param name="itp_input" value="posres.itp" />
152 <param name="mdpfile" value="custom" />
153 <param name="mdp_input" value="nvt.mdp" />
154 <param name="traj" value="none"/>
155 <param name="str" value="gro"/>
156 <output name="output1" file="nvt.gro" ftype="gro" compare="sim_size"/>
157 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
158 </test>
159 </tests>
160 <help><![CDATA[
161
162 Upload GRO, TOP and ITP (position restraint) files for equilibration under an NVT ensemble. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options.
163 ]]></help>
164
165 <expand macro="citations" />
166 </tool>