Mercurial > repos > chemteam > gmx_sim
comparison sim.xml @ 2:5642f48f5698 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author | chemteam |
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date | Wed, 20 Nov 2019 11:13:22 -0500 |
parents | ec3f665cca3e |
children | 4dba9a5b74fc |
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1:ec3f665cca3e | 2:5642f48f5698 |
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3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 #if $mdp.mdpfile == "custom": | 8 |
9 ln -s '$mdp.mdp_input' ./md.mdp && | 9 #if $sets.mdp.mdpfile == "custom": |
10 #end if | 10 ln -s '$sets.mdp.mdp_input' ./md.mdp && |
11 #if $mdp.mdpfile == "default": | 11 #end if |
12 #if $sets.mdp.mdpfile == "default": | |
12 ln -s '$md' ./md.mdp && | 13 ln -s '$md' ./md.mdp && |
13 #end if | 14 #end if |
14 | 15 |
15 ln -s '$gro_input' ./inp.gro && | 16 ln -s '$gro_input' ./inp.gro && |
16 ln -s '$top_input' ./top_input.top && | 17 ln -s '$top_input' ./top_input.top && |
17 | 18 |
18 #if $posres.posres_bool == "true": | 19 #if $inps.itp_in: |
19 ln -s '$posres.itp_inp' ./posres.itp && | 20 ln -s '$inps.itp_in' ./posres.itp && |
20 #end if | 21 #end if |
21 | 22 |
22 #if $cpt_inp.cpt_bool == "yes": | 23 #if $inps.cpt_in: |
23 ln -s '$cpt_inp.cpt_in' ./inp.cpt && | 24 ln -s '$inps.cpt_in' ./inp.cpt && |
24 #end if | 25 #end if |
25 | 26 |
26 #if $ndx_inp.ndx_bool == "yes": | 27 #if $inps.ndx_in: |
27 ln -s '$ndx_inp.ndx_in' ./index.ndx && | 28 ln -s '$inps.ndx_in' ./index.ndx && |
28 #end if | 29 #end if |
29 | 30 |
30 gmx grompp | 31 gmx grompp |
31 -f ./md.mdp | 32 -f ./md.mdp |
32 -c ./inp.gro | 33 -c ./inp.gro |
33 #if $cpt_inp.cpt_bool == "yes": | 34 #if $inps.cpt_in: |
34 -t ./inp.cpt | 35 -t ./inp.cpt |
35 #end if | 36 #end if |
36 #if $posres.posres_bool == "true": | 37 #if $inps.itp_in: |
37 -r ./inp.gro | 38 -r ./inp.gro |
38 #end if | 39 #end if |
39 #if $ndx_inp.ndx_bool == "true": | 40 #if $inps.ndx_in: |
40 -n ./index.ndx | 41 -n ./index.ndx |
41 #end if | 42 #end if |
42 -p ./top_input.top | 43 -p ./top_input.top |
43 -o outp.tpr &>> verbose.txt && | 44 -o outp.tpr &>> verbose.txt && |
44 | 45 |
45 | 46 |
46 gmx mdrun -deffnm outp &>> verbose.txt | 47 gmx mdrun -deffnm outp &>> verbose.txt |
47 | 48 |
48 #if $str == 'pdb' or $str == 'both' | 49 #if $outps.str == 'pdb' or $outps.str == 'both' |
49 && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt | 50 && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt |
50 #end if | 51 #end if |
51 | 52 |
52 && cat md.mdp &>> verbose.txt | 53 && cat md.mdp &>> verbose.txt |
53 | 54 |
54 ]]></command> | 55 ]]></command> |
55 <configfiles> | 56 <configfiles> |
56 <!-- .mdp file for the gromacs simulation --> | 57 <!-- .mdp file for the gromacs simulation --> |
57 <configfile name="md"> | 58 <configfile name="md"> |
58 #if $mdp.mdpfile == 'default': | 59 #if $sets.mdp.mdpfile == 'default': |
59 title = OPLS Lysozyme MD simulation | 60 title = OPLS Lysozyme MD simulation |
60 ; Run parameters | 61 ; Run parameters |
61 integrator = $mdp.integrator ; leap-frog integrator | 62 integrator = $sets.mdp.integrator ; leap-frog integrator |
62 nsteps = $mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns) | 63 nsteps = $sets.mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns) |
63 dt = $mdp.step_length ; 2 fs | 64 dt = $sets.mdp.step_length ; 2 fs |
64 ; Output control | 65 ; Output control |
65 nstxout = $mdp.write_freq ; save coordinates every 10.0 ps | 66 nstxout = $sets.mdp.write_freq ; save coordinates every 10.0 ps |
66 nstvout = $mdp.write_freq ; save velocities every 10.0 ps | 67 nstvout = $sets.mdp.write_freq ; save velocities every 10.0 ps |
67 nstenergy = $mdp.write_freq ; save energies every 10.0 ps | 68 nstenergy = $sets.mdp.write_freq ; save energies every 10.0 ps |
68 nstlog = $mdp.write_freq ; update log file every 10.0 ps | 69 nstlog = $sets.mdp.write_freq ; update log file every 10.0 ps |
69 nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps | 70 nstxout-compressed = $sets.mdp.write_freq ; save compressed coordinates every 10.0 ps |
70 ; nstxout-compressed replaces nstxtcout | 71 ; nstxout-compressed replaces nstxtcout |
71 compressed-x-grps = System ; group(s) to write to the compressed trajectory file | 72 compressed-x-grps = System ; group(s) to write to the compressed trajectory file |
72 ; Bond parameters | 73 ; Bond parameters |
73 continuation = $cpt_inp.cpt_bool ; Restarting after NPT | 74 #if $inps.cpt_in: |
75 continuation = yes ; Restarting after NPT | |
76 #end if | |
74 constraint_algorithm = lincs ; holonomic constraints | 77 constraint_algorithm = lincs ; holonomic constraints |
75 constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained | 78 constraints = $sets.mdp.constraints ; all bonds (even heavy atom-H bonds) constrained |
76 lincs_iter = 1 ; accuracy of LINCS | 79 lincs_iter = 1 ; accuracy of LINCS |
77 lincs_order = 4 ; also related to accuracy | 80 lincs_order = 4 ; also related to accuracy |
78 ; Neighborsearching | 81 ; Neighborsearching |
79 cutoff-scheme = $mdp.cutoffscheme | 82 cutoff-scheme = $sets.mdp.cutoffscheme |
80 ns_type = grid ; search neighboring grid cells | 83 ns_type = grid ; search neighboring grid cells |
81 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme | 84 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme |
82 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off | 85 rcoulomb = $sets.mdp.rcoulomb ; Short-range electrostatic cut-off |
83 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list. | 86 rlist = $sets.mdp.rlist ; Cut-off distance for the short-range neighbor list. |
84 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off | 87 rvdw = $sets.mdp.rvdw ; Short-range Van der Waals cut-off |
85 ; Electrostatics | 88 ; Electrostatics |
86 coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME | 89 coulombtype = $sets.mdp.coulombtype ; method for electrostatics calculations e.g. PME |
87 pme_order = 4 ; cubic interpolation | 90 pme_order = 4 ; cubic interpolation |
88 fourierspacing = 0.16 ; grid spacing for FFT | 91 fourierspacing = 0.16 ; grid spacing for FFT |
89 ; Temperature coupling is on | 92 ; Temperature coupling is on |
90 tcoupl = V-rescale ; modified Berendsen thermostat | 93 tcoupl = V-rescale ; modified Berendsen thermostat |
91 tc-grps = Protein Non-Protein ; two coupling groups - more accurate | 94 tc-grps = Protein Non-Protein ; two coupling groups - more accurate |
92 tau_t = 0.1 0.1 ; time constant, in ps | 95 tau_t = 0.1 0.1 ; time constant, in ps |
93 ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K | 96 ref_t = $sets.mdp.temperature $sets.mdp.temperature ; reference temperature, one for each group, in K |
94 ; Periodic boundary conditions | 97 ; Periodic boundary conditions |
95 pbc = xyz ; 3-D PBC | 98 pbc = xyz ; 3-D PBC |
96 ; Dispersion correction | 99 ; Dispersion correction |
97 DispCorr = EnerPres ; account for cut-off vdW scheme | 100 DispCorr = EnerPres ; account for cut-off vdW scheme |
98 ; Velocity generation | 101 ; Velocity generation |
99 gen_vel = no ; Velocity generation is off | 102 gen_vel = no ; Velocity generation is off |
100 #end if | 103 #end if |
101 #if $posres.posres_bool == "true": | 104 #if $inps.itp_in: |
102 define = -DPOSRES ; position restrain the protein | 105 define = -DPOSRES ; position restrain the protein |
103 refcoord_scaling = com | 106 refcoord_scaling = com |
104 #end if | 107 #end if |
105 #if $ensemble == "nvt": | 108 #if $sets.ensemble == "nvt": |
106 pcoupl = no ; no pressure coupling in NVT | 109 pcoupl = no ; no pressure coupling in NVT |
107 #else: | 110 #else: |
108 ; Pressure coupling is on | 111 ; Pressure coupling is on |
109 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT | 112 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT |
110 pcoupltype = isotropic ; uniform scaling of box vectors | 113 pcoupltype = isotropic ; uniform scaling of box vectors |
117 | 120 |
118 </configfiles> | 121 </configfiles> |
119 <inputs> | 122 <inputs> |
120 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> | 123 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> |
121 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> | 124 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> |
122 <conditional name="cpt_inp"> | 125 |
123 <param name="cpt_bool" type="select" label="Use a checkpoint (CPT) file" help="CPT file from a previous MD run"> | 126 <section name="inps" title="Inputs" expanded="false"> |
124 <option value="yes">Continue simulation from a CPT file</option> | 127 |
125 <option value="no" selected="true">No CPT input</option> | 128 <!-- CPT inp --> |
126 </param> | 129 <!-- <conditional name="cpt_inp"> |
127 <when value="yes"> | 130 <param name="cpt_bool" type="select" label="Use a checkpoint (CPT) file" help="CPT file from a previous MD run"> |
128 <param argument="cpt_in" type="data" format='cpt' label="Checkpoint file"/> | 131 <option value="yes">Continue simulation from a CPT file</option> |
129 </when> | 132 <option value="no" selected="true">No CPT input</option> |
130 <when value="no"/> | 133 </param> |
131 </conditional> | 134 <when value="yes"> |
132 <param name="cpt_out" type="select" label="Produce a checkpoint (CPT) file" help="Produce CPT file for a subsequent MD run"> | 135 <param argument="cpt_in" type="data" format='cpt' label="Checkpoint file"/> |
133 <option value="true">Produce CPT output</option> | 136 </when> |
134 <option value="false" selected="true">No CPT output</option> | 137 <when value="no"/> |
135 </param> | 138 </conditional> --> |
136 | 139 |
137 <conditional name="posres"> | 140 <param argument="cpt_in" type="data" format='cpt' label="Checkpoint (CPT) file" optional="true" help="CPT file from a previous MD run. Leave empty if no checkpoint should be used."/> |
138 <param name="posres_bool" type="select" label="Apply position restraints" help="Used e.g. for equilibration of solvent around a protein" value="false"> | 141 |
139 <option value="true">Apply position restraints</option> | 142 <!-- ITP inp --> |
140 <option value="false" selected="true">No position restraints</option> | 143 <!-- <conditional name="posres"> |
141 </param> | 144 <param name="posres_bool" type="select" label="Apply position restraints" help="Used e.g. for equilibration of solvent around a protein" value="false"> |
142 <when value="true"> | 145 <option value="true">Apply position restraints</option> |
143 <param argument="itp_inp" type="data" format='itp' label="Position restraint (ITP) file"/> | 146 <option value="false" selected="true">No position restraints</option> |
144 </when> | 147 </param> |
145 <when value="false"/> | 148 <when value="true"> |
146 </conditional> | 149 <param argument="itp_in" type="data" format='itp' label="Position restraint (ITP) file"/> |
147 | 150 </when> |
148 <conditional name="ndx_inp"> | 151 <when value="false"/> |
149 <param name="ndx_bool" type="select" label="Use a custom index (ndx) file" help="Use an index file specifying custom atom groups."> | 152 </conditional> --> |
150 <option value="yes">Use custom index file</option> | 153 |
151 <option value="no" selected="true">Use default generated group</option> | 154 <param argument="itp_in" type="data" format='itp' label="Position restraint (ITP) file" optional="true" help="Apply position restraints using a ITP file. Leave empty if no position restraints should be used."/> |
152 </param> | 155 |
153 <when value="yes"> | 156 <!-- NDX inp --> |
154 <param argument="ndx_in" type="data" format='txt' label="Index file"/> | 157 <!-- <conditional name="ndx_inp"> |
155 </when> | 158 <param name="ndx_bool" type="select" label="Use a custom index (ndx) file" help="Use an index file specifying custom atom groups."> |
156 <when value="no"/> | 159 <option value="true">Use custom index file</option> |
157 </conditional> | 160 <option value="false" selected="true">Use default generated group</option> |
158 | 161 </param> |
159 | 162 <when value="true"> |
160 <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)"> | 163 <param argument="ndx_in" type="data" format='ndx' label="Index file"/> |
161 <option value="nvt">Isothermal-isochoric ensemble (NVT)</option> | 164 </when> |
162 <option value="npt">Isothermal-isobaric ensemble (NPT)</option> | 165 <when value="false"/> |
163 </param> | 166 </conditional> --> |
164 | 167 |
165 <expand macro="md_inputs"/> | 168 <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"/> |
169 | |
170 </section> | |
171 | |
172 <section name="outps" title="Outputs" expanded="false"> | |
173 <!-- TRAJ out --> | |
174 <param argument="traj" type="select" label="Trajectory output"> | |
175 <option value='none'>Return no trajectory output</option> | |
176 <option value='xtc'>Return .xtc file (reduced precision)</option> | |
177 <option value='trr'>Return .trr file (full precision)</option> | |
178 <option value='both'>Return both .xtc and .trr files</option> | |
179 </param> | |
180 | |
181 <!-- STR out --> | |
182 <param argument="str" type="select" label="Structure output"> | |
183 <option value='none'>Return no structure output</option> | |
184 <option value='gro'>Return .gro file</option> | |
185 <option value='pdb'>Return .pdb file</option> | |
186 <option value='both'>Return both .gro and .pdb files</option> | |
187 </param> | |
188 | |
189 <!-- CPT out --> | |
190 <param name="cpt_out" type="select" label="Produce a checkpoint (CPT) file" help="Produce CPT file for a subsequent MD run"> | |
191 <option value="true">Produce CPT output</option> | |
192 <option value="false" selected="true">No CPT output</option> | |
193 </param> | |
194 | |
195 <!-- EDR out --> | |
196 <param name="edr_out" type="select" label="Produce an energy (EDR) file" help="Produce file containing energies associated with the simulation"> | |
197 <option value="true">Produce EDR output</option> | |
198 <option value="false" selected="true">No EDR output</option> | |
199 </param> | |
200 | |
201 <!-- XVG out --> | |
202 <param name="xvg_out" type="select" label="Produce XVG output" help="Produce tabular XVG file (e.g. forces from pulling simulations)" > | |
203 <option value="true">Produce XVG output</option> | |
204 <option value="false" selected="true">No XVG output</option> | |
205 </param> | |
206 | |
207 </section> | |
208 | |
209 <section name="sets" title="Settings" expanded="false"> | |
210 <!-- other ... --> | |
211 <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)"> | |
212 <option value="nvt">Isothermal-isochoric ensemble (NVT)</option> | |
213 <option value="npt">Isothermal-isobaric ensemble (NPT)</option> | |
214 </param> | |
215 | |
216 <expand macro="md_inputs"/> | |
217 </section> | |
218 | |
219 <expand macro="log" /> | |
220 | |
166 </inputs> | 221 </inputs> |
167 <outputs> | 222 <outputs> |
168 <data name="output1" format="gro" from_work_dir="outp.gro"> | 223 <data name="output1" format="gro" from_work_dir="outp.gro"> |
169 <filter>str == 'gro' or str == 'both'</filter> | 224 <filter>outps.str == 'gro' or outps.str == 'both'</filter> |
170 </data> | 225 </data> |
171 <data name="output2" format="pdb" from_work_dir="outp.pdb"> | 226 <data name="output2" format="pdb" from_work_dir="outp.pdb"> |
172 <filter>str == 'pdb' or str == 'both'</filter> | 227 <filter>outps.str == 'pdb' or outps.str == 'both'</filter> |
173 </data> | 228 </data> |
174 <data name="output3" format="trr" from_work_dir="outp.trr"> | 229 <data name="output3" format="trr" from_work_dir="outp.trr"> |
175 <filter>traj == 'trr' or traj == 'both'</filter> | 230 <filter>outps.traj == 'trr' or outps.traj == 'both'</filter> |
176 </data> | 231 </data> |
177 <data name="output4" format="xtc" from_work_dir="outp.xtc"> | 232 <data name="output4" format="xtc" from_work_dir="outp.xtc"> |
178 <filter>traj == 'xtc' or traj == 'both'</filter> | 233 <filter>outps.traj == 'xtc' or outps.traj == 'both'</filter> |
179 </data> | 234 </data> |
180 <data name="output5" format="cpt" from_work_dir="outp.cpt"> | 235 <data name="output5" format="cpt" from_work_dir="outp.cpt"> |
181 <filter>cpt_out</filter> | 236 <filter>outps.cpt_out == 'true'</filter> |
182 </data> | 237 </data> |
183 | 238 <data name="output6" format="edr" from_work_dir="outp.edr"> |
184 <data name="report" format="txt" from_work_dir="verbose.txt"> | 239 <filter>outps.edr_out == 'true'</filter> |
185 <filter>capture_log</filter> | 240 </data> |
186 </data> | 241 <collection name="output7" type="list"> |
242 <discover_datasets pattern="(?P<designation>.*)\.xvg" visible="true" directory="." /> | |
243 <filter>outps.xvg_out == 'true'</filter> | |
244 </collection> | |
245 | |
246 <expand macro="log_outputs" /> | |
187 </outputs> | 247 </outputs> |
188 | 248 |
189 <tests> | 249 <tests> |
190 <test> | 250 <test> |
191 <param name="gro_input" value="npt.gro" /> | 251 <param name="gro_input" value="npt.gro" /> |
192 <param name="top_input" value="topol_solv.top" /> | 252 <param name="top_input" value="topol_solv.top" /> |
193 <param name="cpt_bool" value="yes" /> | 253 <!-- <param name="cpt_bool" value="yes" /> --> |
194 <param name="cpt_in" value="npt.cpt" /> | 254 <param name="cpt_in" value="npt.cpt" /> |
195 <param name="mdpfile" value="custom" /> | 255 <param name="mdpfile" value="custom" /> |
196 <param name="mdp_input" value="md.mdp" /> | 256 <param name="mdp_input" value="md.mdp" /> |
197 <param name="ndx_bool" value="no" /> | 257 <!-- <param name="ndx_bool" value="false" /> --> |
198 <param name="traj" value="trr"/> | 258 <param name="traj" value="trr"/> |
199 <param name="str" value="gro"/> | 259 <param name="str" value="gro"/> |
200 <param name="ensemble" value="npt" /> | 260 <param name="ensemble" value="npt" /> |
201 <param name="posres_bool" value="false" /> | 261 <!-- <param name="posres_bool" value="false" /> --> |
202 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 262 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> |
203 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 263 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> |
264 <!-- <output name="output1" ftype="gro"> | |
265 <assert_contents> | |
266 <has_size value="2647999" /> | |
267 </assert_contents> | |
268 </output> | |
269 <output name="output3" ftype="trr"> | |
270 <assert_contents> | |
271 <has_size value="10132584" /> | |
272 </assert_contents> | |
273 </output> --> | |
204 </test> | 274 </test> |
205 | 275 |
206 <test> | 276 <test> |
207 <param name="gro_input" value="npt.gro" /> | 277 <param name="gro_input" value="npt.gro" /> |
208 <param name="top_input" value="topol_solv.top" /> | 278 <param name="top_input" value="topol_solv.top" /> |
209 <param name="cpt_bool" value="yes" /> | 279 <!-- <param name="cpt_bool" value="yes" /> --> |
210 <param name="cpt_in" value="npt.cpt" /> | 280 <param name="cpt_in" value="npt.cpt" /> |
211 <param name="ndx_bool" value="no" /> | 281 <!-- <param name="ndx_bool" value="false" /> --> |
212 <param name="traj" value="trr"/> | 282 <param name="traj" value="trr"/> |
213 <param name="str" value="both"/> | 283 <param name="str" value="both"/> |
214 <expand macro="test_params"/> | 284 <expand macro="test_params"/> |
215 <param name="ensemble" value="npt" /> | 285 <param name="ensemble" value="npt" /> |
216 <param name="posres_bool" value="false" /> | 286 <!-- <param name="posres_bool" value="false" /> --> |
217 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 287 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> |
218 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> | 288 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> |
219 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 289 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> |
220 </test> | 290 </test> |
221 | 291 |
222 <test> | 292 <test> |
223 <param name="gro_input" value="npt.gro" /> | 293 <param name="gro_input" value="npt.gro" /> |
224 <param name="top_input" value="topol_solv.top" /> | 294 <param name="top_input" value="topol_solv.top" /> |
225 <param name="cpt_bool" value="yes" /> | 295 <!-- <param name="cpt_bool" value="yes" /> --> |
226 <param name="cpt_in" value="npt.cpt" /> | 296 <param name="cpt_in" value="npt.cpt" /> |
227 <param name="ndx_bool" value="yes" /> | 297 <!-- <param name="ndx_bool" value="true" /> --> |
228 <param name="ndx_in" value="index.ndx" /> | 298 <param name="ndx_in" value="index.ndx" /> |
229 <param name="traj" value="trr"/> | 299 <param name="traj" value="trr"/> |
230 <param name="str" value="both"/> | 300 <param name="str" value="both"/> |
231 <expand macro="test_params"/> | 301 <expand macro="test_params"/> |
232 <param name="ensemble" value="npt" /> | 302 <param name="ensemble" value="npt" /> |
233 <param name="posres_bool" value="false" /> | 303 <!-- <param name="posres_bool" value="false" /> --> |
234 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 304 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> |
235 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> | 305 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> |
236 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 306 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> |
237 </test> | 307 </test> |
238 | 308 |
239 <test> | 309 <test> |
240 <param name="gro_input" value="em.gro" /> | 310 <param name="gro_input" value="em.gro" /> |
241 <param name="top_input" value="topol_solv.top" /> | 311 <param name="top_input" value="topol_solv.top" /> |
242 <param name="posres_bool" value="true" /> | 312 <!-- <param name="posres_bool" value="true" /> --> |
243 <param name="itp_inp" value="posres.itp" /> | 313 <param name="itp_in" value="posres.itp" /> |
244 <param name="cpt_bool" value="no" /> | 314 <!-- <param name="cpt_bool" value="no" /> --> |
245 <param name="cpt_out" value="true" /> | 315 <param name="cpt_out" value="true" /> |
246 <param name="ndx_bool" value="no" /> | 316 <!-- <param name="ndx_bool" value="false" /> --> |
247 <param name="traj" value="xtc"/> | 317 <param name="traj" value="xtc"/> |
248 <param name="str" value="pdb"/> | 318 <param name="str" value="pdb"/> |
249 <param name="ensemble" value="nvt" /> | 319 <param name="ensemble" value="nvt" /> |
250 <expand macro="test_params"/> | 320 <expand macro="test_params"/> |
251 | 321 |