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comparison alchemical_run/gmx_fep.xml @ 0:19d1d4c30402 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
author chemteam
date Mon, 11 Nov 2019 13:20:39 -0500
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1 <tool id="gmx_fep" name="Alchemical Run" version="2019.1">
2 <description>Alchemical free energy simulations using gromacs</description>
3 <requirements>
4 <requirement type="package" version="2019.1">gromacs</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 ln -s '$em_steep' ./em_steep.mdp &&
8 ln -s '$nvt' ./nvt.mdp &&
9 ln -s '$npt' ./npt.mdp &&
10 ln -s '$md' ./md.mdp &&
11
12 ln -s '$groin' ./morph.gro &&
13 ln -s '$topin' ./morph.top &&
14
15 #if $input_fep == 'perform':
16 bash '$__tool_directory__/gmx_fep.sh' '$path.lambda' &>> '$report'
17 #end if
18 #if $input_fep == 'generate':
19 mkdir -p input_files &&
20 cp '$__tool_directory__/gmx_fep.sh' input_files/ &&
21 cp ./em_steep.mdp input_files/ &&
22 cp ./nvt.mdp input_files/ &&
23 cp ./npt.mdp input_files/ &&
24 cp ./md.mdp input_files/ &&
25 cp ./morph.gro input_files/ &&
26 cp ./morph.top input_files/ &&
27 tar cf input_files.tar input_files/
28 #end if
29 ]]></command>
30 <configfiles>
31 <configfile name="em_steep">
32 integrator = steep
33 nsteps = $minstep
34 emtol = 100
35 emstep = 0.01
36 niter = 20
37 nbfgscorr = 10
38 nstlog = 1
39 nstenergy = 1
40 cutoff-scheme = verlet
41 nstlist = 10
42 ns_type = grid
43 pbc = xyz
44 rlist = 1.2
45 coulombtype = PME
46 rcoulomb = 1.2
47 vdwtype = cutoff
48 vdw-modifier = potential-switch
49 rvdw-switch = 1.0
50 rvdw = 1.2
51 DispCorr = EnerPres
52 fourierspacing = 0.12
53 pme_order = 6
54 ewald_rtol = 1e-06
55 epsilon_surface = 0
56 tcoupl = no
57 pcoupl = no
58 ld-seed = -1
59 gen-seed = $seed
60 free_energy = no
61 delta_lambda = 0
62 calc_lambda_neighbors = 1
63 init-lambda-state = %L%
64
65 #if $path.select_path == "global":
66 fep-lambdas = $path.fep
67 #end if
68
69 #if $path.select_path in ["default1", "default2"]:
70 coul-lambdas = $path.coul
71 vdw-lambdas = $path.vdw
72 bonded-lambdas = $path.bonded
73 #end if
74
75 sc-alpha = 0.5
76 sc-coul = no
77 sc-power = 1
78 sc-sigma = 0.3
79 nstdhdl = 10
80
81 gen_vel = no
82 constraints = none
83 </configfile>
84 <configfile name="nvt">
85 integrator = sd
86 tinit = 0
87 dt = $dt
88 nsteps = $nvtstep
89 nstcomm = 100
90 nstxout = 500
91 nstvout = 500
92 nstfout = 0
93 nstlog = 500
94 nstenergy = 500
95 nstxout-compressed = 0
96 cutoff-scheme = verlet
97 nstlist = 20
98 ns_type = grid
99 pbc = xyz
100 rlist = 1.2
101 coulombtype = PME
102 rcoulomb = 1.2
103 vdwtype = cutoff
104 vdw-modifier = potential-switch
105 rvdw-switch = 1.0
106 rvdw = 1.2
107 DispCorr = EnerPres
108 fourierspacing = 0.12
109 pme_order = 6
110 ewald_rtol = 1e-06
111 epsilon_surface = 0
112 tc_grps = system
113 tau_t = 1.0
114 ref_t = $temperature
115 Pcoupl = No
116 tau_p = 0.5
117 compressibility = 4.5e-05
118 ref_p = $pressure
119 ld-seed = -1
120 gen-seed = $seed
121 free_energy = no
122 delta_lambda = 0
123 calc_lambda_neighbors = 1
124 init-lambda-state = %L%
125
126 #if $path.select_path == "global":
127 fep-lambdas = $path.fep
128 #end if
129
130 #if $path.select_path in ["default1", "default2"]:
131 coul-lambdas = $path.coul
132 vdw-lambdas = $path.vdw
133 bonded-lambdas = $path.bonded
134 #end if
135
136 sc-alpha = 0.5
137 sc-coul = no
138 sc-power = 1
139 sc-sigma = 0.3
140 nstdhdl = 10
141 gen_vel = yes
142 gen_temp = 300
143
144 #if $constraints.cons == "no":
145 constraints = none
146 #end if
147
148 #if $constraints.cons == "yes":
149 constraints = $constraints.cons_type
150 constraint-algorithm = lincs
151 lincs-order = $constraints.lincs_order
152 lincs-iter = $constraints.lincs_iter
153 lincs-warnangle = $constraints.lincs_warnangle
154 #end if
155 </configfile>
156 <configfile name="npt">
157 integrator = sd
158 tinit = 0
159 dt = $dt
160 nsteps = $nptstep
161 nstcomm = 100
162 nstxout = 500
163 nstvout = 500
164 nstfout = 0
165 nstlog = 500
166 nstenergy = 500
167 nstxout-compressed = 0
168 cutoff-scheme = verlet
169 nstlist = 20
170 ns_type = grid
171 pbc = xyz
172 rlist = 1.2
173 coulombtype = PME
174 rcoulomb = 1.2
175 vdwtype = cutoff
176 vdw-modifier = potential-switch
177 rvdw-switch = 1.0
178 rvdw = 1.2
179 DispCorr = EnerPres
180 fourierspacing = 0.12
181 pme_order = 6
182 ewald_rtol = 1e-06
183 epsilon_surface = 0
184 tc_grps = System
185 tau_t = 1.0
186 ref_t = $temperature
187 Pcoupl = Berendsen
188 tau_p = 0.5
189 compressibility = 4.5e-05
190 ref_p = $pressure
191 ld-seed = -1
192 gen-seed = $seed
193 free_energy = no
194 delta_lambda = 0
195 calc_lambda_neighbors = 1
196 init-lambda-state = %L%
197
198 #if $path.select_path == "global":
199 fep-lambdas = $path.fep
200 #end if
201
202 #if $path.select_path in ["default1", "default2"]:
203 coul-lambdas = $path.coul
204 vdw-lambdas = $path.vdw
205 bonded-lambdas = $path.bonded
206 #end if
207
208 ; Options for the decoupling
209 sc-alpha = 0.5
210 sc-coul = no
211 sc-power = 1
212 sc-sigma = 0.3
213 nstdhdl = 10
214 gen_vel = no
215
216 #if $constraints.cons == "no":
217 constraints = none
218 #end if
219
220 #if $constraints.cons == "yes":
221 constraints = $constraints.cons_type
222 constraint-algorithm = lincs
223 lincs-order = $constraints.lincs_order
224 lincs-iter = $constraints.lincs_iter
225 lincs-warnangle = $constraints.lincs_warnangle
226 #end if
227 </configfile>
228 <configfile name="md">
229 integrator = sd
230 bd-fric = 0
231 dt = $dt
232 nsteps = $mdstep
233 nstcomm = 100
234
235 nstxout = 10000
236 nstvout = 0
237 nstfout = 0
238 nstlog = 10000
239 nstenergy = 10000
240 nstxout-compressed = 0
241
242 tcoupl = no
243 nsttcouple = 10
244 tc_grps = System
245 tau_t = 1.0
246 ref_t = $temperature
247
248 #if $constraints.cons == "no":
249 constraints = none
250 #end if
251
252 #if $constraints.cons == "yes":
253 constraints = $constraints.cons_type
254 constraint-algorithm = lincs
255 lincs-order = $constraints.lincs_order
256 lincs-iter = $constraints.lincs_iter
257 lincs-warnangle = $constraints.lincs_warnangle
258 #end if
259
260 comm-mode = Linear
261
262 cutoff-scheme = Verlet
263 nstlist = 10
264 ns_type = grid
265 pbc = xyz
266 rlist = 0.8
267
268 coulombtype = PME
269 coulomb-modifier = none
270 rcoulomb = 0.8
271 fourierspacing = 0.10
272 pme_order = 4
273 ewald_rtol = 1.0E-5
274
275 vdwtype = cut-off
276 vdw-modifier = none
277 rvdw = 0.8
278 DispCorr = AllEnerPres
279
280 pcoupl = Parrinello-Rahman
281 pcoupltype = isotropic
282 tau_p = 2
283 compressibility = 4.5e-5
284 ref_p = $pressure
285 refcoord-scaling = com
286
287 gen-vel = no
288 continuation = yes
289
290 ld-seed = -1
291 gen-seed = $seed
292
293 free-energy = yes
294 delta-lambda = 0 ; do not use slow growth method
295 init-lambda-state = %L%
296
297 #if $path.select_path == "global":
298 fep-lambdas = $path.fep
299 #end if
300
301 #if $path.select_path in ["default1", "default2"]:
302 coul-lambdas = $path.coul
303 vdw-lambdas = $path.vdw
304 bonded-lambdas = $path.bonded
305 #end if
306
307 nstdhdl = 10
308 nstcalcenergy = 10
309 calc-lambda-neighbors = -1
310
311 #if $feoptions.feop == "default":
312 sc-alpha = 0.5
313 sc-coul = no
314 sc-power = 1
315 sc-r-power = 6
316 sc-sigma = 0.3
317 couple-lambda0 = vdw-q
318 couple-lambda1 = none
319 couple-intramol = no
320 #end if
321
322 #if $feoptions.feop == "modify":
323 sc-alpha = $feoptions.scalpha
324 sc-coul = $feoptions.sccoul
325 sc-power = $feoptions.scpower
326 sc-r-power = $feoptions.scrpower
327 sc-sigma = $feoptions.scsigma
328 couple-lambda0 = $feoptions.couplelambda0
329 couple-lambda1 = $feoptions.couplelambda1
330 couple-intramol = $feoptions.coupleintramol
331 #end if
332
333 dhdl-derivatives = yes
334 dhdl-print-energy = no
335 separate-dhdl-file = yes
336 dh_hist_size = 0
337 dh_hist_spacing = 0.1
338
339 </configfile>
340 </configfiles>
341 <inputs>
342 <param format="gro" name="groin" type="data" label="Structure (GRO) file" help="GRO input file with the merged structure."/>
343 <param format="top" name="topin" type="data" label="Topology (TOP) file" help="TOP input file with the merged structure."/>
344 <param name="minstep" type="integer" value="10000" label="Minimization steps" help="Number of steps for each free energy window."/>
345 <param name="nvtstep" type="integer" value="500000" label="NVT equilibration steps" help="Number of MD steps for NVT equilibration for each free energy window."/>
346 <param name="nptstep" type="integer" value="500000" label="NPT equilibration steps" help="Number of MD steps for NPT equilibration for each free energy window."/>
347 <param name="mdstep" type="integer" value="1000000" label="MD (production) steps" help="Number of MD steps for production runs of each free energy window."/>
348 <param name="seed" type="integer" value="19880924" label="Seed" help="Seed to initialize random generator for random velocities."/>
349 <param name="dt" type="float" value="0.001" label="Time step (ps)" help="Time step for integration."/>
350 <conditional name="constraints">
351 <param name="cons" type="select" label="Apply constraints to the ligands?" help="Constraints may be required to keep the ligands with alchemical states in the active site.">
352 <option value="yes">Yes</option>
353 <option value="no">No</option>
354 </param>
355 <when value="no"/>
356 <when value="yes">
357 <param name="cons_type" type="select" label="Constraints type" help="Convert all bonds to constraints, or only those containing hydrogen atoms">
358 <option value="h-bonds" selected="true">H-bonds</option>
359 <option value="all-bonds">All bonds</option>
360 </param>
361 <param name="lincs_order" type="integer" value="4" label="LINCS order" help="Accuracy of LINCS algorithm. For normal MD simulations an order of 4 usually suffices, 6 is needed for large time-steps with virtual sites or BD."/>
362 <param name="lincs_iter" type="integer" value="1" label="LINCS iterations" help="Number of iterations to correct for rotational lengthening in LINCS. For normal runs a single step is sufficient."/>
363 <param name="lincs_warnangle" type="integer" value="30" label="LINCS maximum angle" help="Maximum angle that a bond can rotate before LINCS will complain / [deg]"/>
364 </when>
365 </conditional>
366 <conditional name="path">
367 <param name="select_path" type="select" label="Select the FEP path">
368 <option value="global">Use global lambda scaling</option>
369 <option value="default1">Default option 1 (change a larger ligand to a smaller ligand)</option>
370 <option value="default2">Default option 2 (change a smaller ligand to a larger ligand)</option>
371 </param>
372 <when value="global">
373 <param name="lambda" type="text" value="2" label="Number of free energy windows"/>
374 <param name="fep" type="text" value="0.00 0.50 1.00" label="FEP Lambdas" help="Global scaling - values must be between 0 and 1."/>
375 </when>
376 <when value="default1">
377 <param name="lambda" type="text" value="40" label="Number of free energy windows"/>
378 <param name="coul" type="text" value="0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.000 1.00" label="Coulomb Lambdas (scaling electrostatics)" help="Values must be between 0 and 1."/>
379 <param name="vdw" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00" label="Van der Waals Lambdas (scaling vdw interactions)" help="Values must be between 0 and 1."/>
380 <param name="bonded" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00" label="Bonded Lambdas (scaling torsion)" help="Values must be between 0 and 1."/>
381 </when>
382 <when value="default2">
383 <param name="lambda" type="text" value="40" label="Number of free energy windows"/>
384 <param name="coul" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00 " label="Coulomb Lambdas (scaling electrostatics)" help="Values must be between 0 and 1."/>
385 <param name="vdw" type="text" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00" label="Van der Waals Lambdas (scaling vdw interactions)" help="Values must be between 0 and 1."/>
386 <param name="bonded" type="text" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00" label="Bonded Lambdas (scaling torsion)" help="Values must be between 0 and 1."/>
387 </when>
388 </conditional>
389 <conditional name="feoptions">
390 <param name="feop" type="select" label="Free energy variables">
391 <option value="default">Use default options</option>
392 <option value="modify">Modify default options</option>
393 </param>
394 <when value="default"/>
395 <when value="modify">
396 <param name="scalpha" type="float" value="0.5" label="The soft-core alpha parameter (sc-alpha)" />
397 <param name="scrpower" type="integer" value="6" label="The power of the radial term in the soft-core equation (sc-r-power)" />
398 <param name="scpower" type="integer" value="1" label="The power for lambda in the soft-core function (sc-power)" />
399 <param name="sccoul" type="text" value="no" label="Apply the soft-core free energy interaction transformation to the Columbic interaction of a molecule (sc-coul)? "/>
400 <param name="scsigma" type="float" value="0.3" label="The soft-core sigma" />
401 <param name="couplelambda0" type="text" value="vdw-q" label="Interactions at lambda=0" help="options are vdw-q, vdw, q, or none"/>
402 <param name="couplelambda1" type="text" value="none" label="Interactions at lambda=1" help="options are vdw-q, vdw, q, or none"/>
403 <param name="coupleintramol" type="text" value="no" label="Turn off intra-molecular interactions?" />
404 </when>
405 </conditional>
406 <param name="temperature" type="float" value="300.0" label="Temperature /K" />
407 <param name="pressure" type="float" value="1.0" label="Pressure /bar" />
408 <param name="input_fep" type="select" label="Perform simulation or only generate input files?">
409 <option value="perform">Perform simulation</option>
410 <option value="generate">Only generate input files</option>
411 </param>
412 </inputs>
413 <outputs>
414 <data name="fepinpout" format="tar" from_work_dir="input_files.tar" label="Input files">
415 <filter>input_fep == 'generate'</filter>
416 </data>
417 <data name="dataout" format="tar" from_work_dir="data.tar" label="TI/FEP data output">
418 <filter>input_fep == 'perform'</filter>
419 </data>
420 <data name="trajout" format="tar" from_work_dir="traj.tar" label="Trajectories output">
421 <filter>input_fep == 'perform'</filter>
422 </data>
423 <data name="report" format="txt" label="Report">
424 <filter>input_fep == 'perform'</filter>
425 </data>
426 </outputs>
427 <tests>
428 <test>
429 <param name="groin" value="morph.gro" ftype="gro"/>
430 <param name="topin" value="morph.top" ftype="top"/>
431 <param name="minstep" value="10"/>
432 <param name="nvtstep" value="50"/>
433 <param name="nptstep" value="50"/>
434 <param name="mdstep" value="100"/>
435 <param name="seed" value="19880924"/>
436 <param name="cons" value="no"/>
437 <param name="dt" value="0.001"/>
438 <param name="path" value="global"/>
439 <param name="lambda" value="2"/>
440 <param name="fep" value="0.00 0.50 1.00"/>
441 <param name="temperature" value="300.0"/>
442 <param name="fepop" value="default"/>
443 <param name="input_fep" value="perform"/>
444 <param name="pressure" value="1.0"/>
445 <output name="dataout" file="TI_FEP_data_output.tar" compare="sim_size"/>
446 </test>
447 <test>
448 <param name="groin" value="morph.gro" ftype="gro"/>
449 <param name="topin" value="morph.top" ftype="top"/>
450 <param name="minstep" value="10000"/>
451 <param name="nvtstep" value="500000"/>
452 <param name="nptstep" value="500000"/>
453 <param name="mdstep" value="1000000"/>
454 <param name="seed" value="123546"/>
455 <param name="cons" value="yes"/>
456 <param name="cons_type" value="h-bonds"/>
457 <param name="lincs_order" value="4"/>
458 <param name="lincs_iter" value="1"/>
459 <param name="incs_warnangle" value="30"/>
460 <param name="dt" value="0.002"/>
461 <param name="path" value="default2"/>
462 <param name="lambda" value="40"/>
463 <param name="coul" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00"/>
464 <param name="vdw" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00"/>
465 <param name="bonded" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00"/>
466 <param name="temperature" value="300.0"/>
467 <param name="fepop" value="default"/>
468 <param name="input_fep" value="generate"/>
469 <param name="pressure" value="1.0"/>
470 <output name="fepinpout" file="Input_files.tar" compare="sim_size"/>
471 </test>
472 </tests>
473 <help><![CDATA[
474 .. class:: infomark
475
476 **What it does**
477
478
479 - This tool can run the alchemical free energy calculations using GROMACS.
480 - For more details about alchemical free energy calculations see http://www.alchemistry.org/wiki/Main_Page
481 - For details about GROMACS simulations see http://manual.gromacs.org/documentation/2019-rc1/user-guide/mdp-options.html
482
483 When you need to run the simulation outside Galaxy, you can generate and down load all the input files from this tool.
484
485 1. Simply download the output "Input files".
486 2. Untar it using tar -xvf Galaxy3-\[Input_files\].tar
487 3. Run the bash script inside ./gmx_fep.sh {number of FEP windows}
488 - Give the number of FEP windows as an argument.
489
490 This will generate input .MDP files and run all the steps for all the FEP windows iteratively.
491
492
493 _____
494
495
496 .. class:: infomark
497
498 **Rules of Thumb for Intermediate States (taken from alchemistry.org)**
499
500 - These rules are not the end-all set and you should be familiar with why each one is suggested before just accepting them.
501 - Bonded terms can be modified/turned off linearly. This includes angle or bond force constants as well as unconstrained bond distances.
502 - Constrained bonds should not change length. There are free energy changes that cannot be ignored affiliated with this action.
503 - Maximize similarity between states by removing/decoupling as few atoms as possible.
504 - Do not open and close rings. This supersedes the previous rule.
505 - Statistical uncertainty between any neighboring states should be equal. Rather challenging to do, but it has been proven to have the lowest variance path if you can pull it off.
506 - Deleting or adding atoms should always be done with a soft core potential.
507 - Changes in parameters can be done linearly.
508 - All charge on atoms must be turned off prior to atomic repulsion. Otherwise you can get an infinite attractive potential and crash your simulation.
509 - Similarly for only changes in terms, it's generally more efficient to change electrostatic terms separate from Lennard-Jones terms.
510 - More states is better than fewer. Variance shrinks rapidly with number of states. You want the difference between intermediaries to be between 2-3 kBT
511
512 Obviously you will be limited on CPU power. Fewer states also leads to more samples begin required from each state, so take this into account when deciding number of states as well.
513 However, for MBAR and TI, it can be shown that spreading samples across multiple states does not significantly affect the uncertainty, since for TI, each state contributes less to
514 the total uncertainty, and in MBAR, data contributes to the statistical precision of states with similar values of lambda.
515
516 Shape of the variance does not significantly change with number of atoms, only magnitude. More intermediates will still be required for a large number of atoms to reduce statistical noise.
517 Charge should be maintained across all λ
518
519 Simply having charged molecules is fine, but the net of the system should remain constant. If you must change the net charge, there are complicated ways to do so.
520
521 Short prototype simulations are recommended. Even as short as 100 ps, the prototypes can provide rough magnitude of variance estimates,
522 although will likely under-predict the free energy as many configurations remain unsampled.
523
524
525 _____
526
527
528 .. class:: infomark
529
530 **Input**
531
532 - .GRO input
533 - .TOP input
534
535 _____
536
537
538 .. class:: infomark
539
540 **Output**
541
542 - TI/FEP data
543 - TI/FEP trajectory
544 - Report
545
546 ]]></help>
547 <citations>
548 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
549 <citation type="bibtex">@misc{alchemistrywiki, title={Alchemistry.org}, url={http://www.alchemistry.org/wiki/Main_Page}, journal={AlchemistryWiki}}
550 </citation>
551 </citations>
552 </tool>