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comparison sim.xml @ 2:c22ee25f4092 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 16:06:27 +0000
parents 9f9b35ba9882
children 83d787befb8b
comparison
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1:9f9b35ba9882 2:c22ee25f4092
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&lt;designation&gt;.*)\.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