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comparison md.xml @ 0:d97433b7d482 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
author chemteam
date Thu, 04 Oct 2018 18:23:17 -0400
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children 609d93596b61
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-1:000000000000 0:d97433b7d482
1 <tool id="gmx_md" name="GROMACS production simulation" version="@VERSION@">
2 <description>for data collection</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 #if $mdp.mdpfile == "custom":
9 ln -s '$mdp.mdp_input' ./md.mdp &&
10 #end if
11 #if $mdp.mdpfile == "default":
12 ln -s '$md' ./md.mdp &&
13 #end if
14
15 ln -s '$gro_input' ./npt.gro &&
16 ln -s '$cpt_input' ./npt.cpt &&
17 ln -s '$top_input' ./top_input.top &&
18
19
20 gmx grompp -f ./md.mdp -c ./npt.gro -t ./npt.cpt -p ./top_input.top -o md_0_1.tpr &>> verbose.txt &&
21 gmx mdrun -deffnm md_0_1 &>> verbose.txt
22
23 #if $str == 'pdb' or $str == 'both'
24 && gmx editconf -f md_0_1.gro -o md_0_1.pdb &>> verbose.txt
25 #end if
26
27
28 ]]></command>
29 <configfiles>
30 <!-- .mdp file for the gromacs simulation -->
31 <configfile name="md">
32 #if $mdp.mdpfile == 'default':
33 title = OPLS Lysozyme MD simulation
34 ; Run parameters
35 integrator = $mdp.integrator ; leap-frog integrator
36 nsteps = $mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns)
37 dt = $mdp.step_length ; 2 fs
38 ; Output control
39 nstxout = $mdp.write_freq ; save coordinates every 10.0 ps
40 nstvout = $mdp.write_freq ; save velocities every 10.0 ps
41 nstenergy = $mdp.write_freq ; save energies every 10.0 ps
42 nstlog = $mdp.write_freq ; update log file every 10.0 ps
43 nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps
44 ; nstxout-compressed replaces nstxtcout
45 compressed-x-grps = System ; group(s) to write to the compressed trajectory file
46 ; Bond parameters
47 continuation = yes ; Restarting after NPT
48 constraint_algorithm = lincs ; holonomic constraints
49 constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained
50 lincs_iter = 1 ; accuracy of LINCS
51 lincs_order = 4 ; also related to accuracy
52 ; Neighborsearching
53 cutoff-scheme = $mdp.cutoffscheme
54 ns_type = grid ; search neighboring grid cells
55 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
56 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
57 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
58 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
59 ; Electrostatics
60 coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME
61 pme_order = 4 ; cubic interpolation
62 fourierspacing = 0.16 ; grid spacing for FFT
63 ; Temperature coupling is on
64 tcoupl = V-rescale ; modified Berendsen thermostat
65 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
66 tau_t = 0.1 0.1 ; time constant, in ps
67 ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K
68 ; Pressure coupling is on
69 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
70 pcoupltype = isotropic ; uniform scaling of box vectors
71 tau_p = 2.0 ; time constant, in ps
72 ref_p = 1.0 ; reference pressure, in bar
73 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
74 ; Periodic boundary conditions
75 pbc = xyz ; 3-D PBC
76 ; Dispersion correction
77 DispCorr = EnerPres ; account for cut-off vdW scheme
78 ; Velocity generation
79 gen_vel = no ; Velocity generation is off
80 #end if
81 </configfile>
82
83 </configfiles>
84 <inputs>
85 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
86 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
87 <param argument="cpt_input" type="data" format='cpt' label="Checkpoint (CPT) file from NVT run."/>
88
89 <expand macro="md_inputs"/>
90 </inputs>
91 <outputs>
92 <data name="output1" format="gro" from_work_dir="md_0_1.gro">
93 <filter>str == 'gro' or str == 'both'</filter>
94 </data>
95 <data name="output2" format="pdb" from_work_dir="md_0_1.pdb">
96 <filter>str == 'pdb' or str == 'both'</filter>
97 </data>
98 <data name="output3" format="trr" from_work_dir="md_0_1.trr">
99 <filter>traj == 'trr' or traj == 'both'</filter>
100 </data>
101 <data name="output4" format="xtc" from_work_dir="md_0_1.xtc">
102 <filter>traj == 'xtc' or traj == 'both'</filter>
103 </data>
104
105 <data name="report" format="txt" from_work_dir="verbose.txt">
106 <filter>capture_log</filter>
107 </data>
108 </outputs>
109 <tests>
110 <test>
111 <param name="gro_input" value="npt.gro" />
112 <param name="top_input" value="topol_solv.top" />
113 <param name="cpt_input" value="npt.cpt" />
114 <param name="traj" value="trr"/>
115 <param name="str" value="both"/>
116
117 <expand macro="test_params"/>
118
119 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
120 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
121 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
122 </test>
123 <test>
124 <param name="gro_input" value="npt.gro" />
125 <param name="top_input" value="topol_solv.top" />
126 <param name="cpt_input" value="npt.cpt" />
127 <param name="itp_input" value="posres.itp" />
128 <param name="traj" value="xtc"/>
129 <param name="str" value="pdb"/>
130
131 <expand macro="test_params"/>
132
133 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
134 <output name="output4" file="md_0_1.xtc" ftype="xtc" compare="sim_size"/>
135 </test>
136 <test>
137 <param name="gro_input" value="npt.gro" />
138 <param name="top_input" value="topol_solv.top" />
139 <param name="cpt_input" value="npt.cpt" />
140 <param name="mdpfile" value="custom" />
141 <param name="mdp_input" value="md.mdp" />
142 <param name="traj" value="trr"/>
143 <param name="str" value="gro"/>
144 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
145 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
146 </test>
147 </tests>
148 <help><![CDATA[
149
150 Upload GRO and TOP files for the production simulation, as well as the checkpoint (CPT) file from the NPT equilibration. 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/online/mdp_opt.html for more information on the options.
151 ]]></help>
152
153 <expand macro="citations" />
154 </tool>