1g_wham(1) GROMACS suite, VERSION 4.5 g_wham(1)
2
6 g_wham - weighted histogram analysis after umbrella sampling
7 VERSION 4.5
9
11 g_wham -ix pullx-files.dat -if pullf-files.dat -it tpr-files.dat -ip
12 pdo-files.dat -o profile.xvg -hist histo.xvg -bsres bsResult.xvg
13 -bsprof bsProfs.xvg -tab umb-pot.dat -wcorr cycl-corr.xvg -[no]h
14 -[no]version -nice int -xvg enum -min real -max real -[no]auto -bins
15 int -temp real -tol real -[no]v -b real -e real -dt real -[no]histonly
16 -[no]boundsonly -[no]log -unit enum -zprof0 real -cycl enum -alpha real
17 -[no]flip -[no]hist-eq -nBootstrap int -bs-dt real -bs-seed int
18 -[no]histbs -histbs-block int -[no]vbs
19
21 This is an analysis program that implements the Weighted Histogram
22 Analysis Method (WHAM). It is intended to analyze output files gener‐
23 ated by umbrella sampling simulations to compute a potential of mean
24 force (PMF).
25 At present, three input modes are supported:
28 * With option -it, the user provides a file which contains the
30 filenames of the umbrella simulation run-input files (tpr files),
31 AND, with option -ix, a file which contains filenames of the pullx
32 mdrun output files. The tpr and pullx files must be in corresponding
33 order, i.e. the first tpr created the first pullx, etc.
34 * Same as the previous input mode, except that the the user provides
36 the pull force ouput file names (pullf.xvg) with option -if. From
37 the pull force the position in the ubrella potential is computed.
38 This does not work with tabulated umbrella potentials. * With option
39 -ip, the user provides filenames of (gzipped) pdo files, i.e. the
40 gromacs 3.3 umbrella output files. If you have some unusual reaction
41 coordinate you may also generate your own pdo files and feed them
42 with the -ip option into to g_wham. The pdo file header must be simi‐
43 lar to the folowing:
44 UMBRELLA 3.0
46 Component selection: 0 0 1
48 nSkip 1
50 Ref. Group 'TestAtom'
52 Nr. of pull groups 2
54 Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0
56 Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0
58 Nr of pull groups, umbrella positions, force constants, and names
62 may (of course) differ. Following the header, a time column and a
63 data columns for each pull group follow (i.e. the displacement with
64 respect to the umbrella center). Up to four pull groups are possible
65 at present.
66 By default, the output files are
69 -o PMF output file
71 -hist histograms output file
73 The umbrella potential is assumed to be harmonic and the force con‐
76 stants are read from the tpr or pdo files. If a non-harmonic umbrella
77 force was applied a tabulated potential can be provied with -tab.
78 WHAM OPTIONS
81 -bins Nr of bins used in analysis
84 -temp Temperature in the simulations
86 -tol Stop iteration if profile (probability) changed less than
88 tolerance
89 -auto Automatic determination of boudndaries
91 -min,-max Boundaries of the profile
93 The data points which are used to compute the profile can be restricted
95 with options -b, -e, and -dt. Play particularly with -b to ensure suf‐
96 ficient equilibration in each umbrella window!
97 With -log (default) the profile is written in energy units, otherwise
100 (-nolog) as probability. The unit can be specified with -unit. With
101 energy output, the energy in the first bin is defined to be zero. If
102 you want the free energy at a different position to be zero, choose
103 with -zprof0 (useful with bootstrapping, see below).
104 For cyclic (or periodic) reaction coordinates (dihedral angle, channel
107 PMF without osmotic gradient), -cycl is useful.
108 -cycl yes min and max are assumed to be neighboring points and
110 histogram points outside min and max are mapped into the interval
111 [min,max] (compare histogram output).
112 -cycl weighted First, a non-cyclic profile is computed. Subse‐
114 quently, periodicity is enforced by adding corrections dG(i) between
115 neighboring bins i and i+1. The correction is chosen proportional to
116 1/[n(i)*n(i+1)]alpha, where n(i) denotes the total nr of data points in
117 bin i as collected from all histograms. alpha is defined with -alpha.
118 The corrections are written to the file defined by -wcorr. (Compare
119 Hub and de Groot, PNAS 105:1198 (2008))
120 ERROR ANALYSIS
123 Statistical errors may be estimated with bootstrap analysis. Use it
125 with care, otherwise the statistical error may be substantially under‐
126 erstimated !!
127 -nBootstrap defines the nr of bootstraps. Two bootstrapping modes are
129 supported.
130 -histbs Complete histograms are considered as independent data
132 points (default). For each bootstrap, N histograms are randomly chosen
133 from the N given histograms (allowing duplication). To avoid gaps
134 without data along the reaction coordinate blocks of histograms
135 (-histbs-block) may be defined. In that case, the given histograms are
136 divided into blocks and only histograms within each block are mixed.
137 Note that the histograms within each block must be representative for
138 all possible histograms, otherwise the statistical error is underersti‐
139 mated!
140 -nohistbs The given histograms are used to generate new random his‐
142 tograms, such that the generated data points are distributed according
143 the given histograms. The number of points generated for each bootstrap
144 histogram can be controlled with -bs-dt. Note that one data point
145 should be generated for each *independent* point in the given his‐
146 tograms. With the long autocorrelations in MD simulations, this proce‐
147 dure may easily understimate the error!
148 Bootstrapping output:
150 -bsres Average profile and standard deviations
152 -bsprof All bootstrapping profiles
154 With -vbs (verbose bootstrapping), the histograms of each bootstrap
156 are written, and, with -nohistBS, the cummulants of the histogram.
157
159 -ix pullx-files.dat Input, Opt.
160 Generic data file
161 -if pullf-files.dat Input, Opt.
163 Generic data file
164 -it tpr-files.dat Input, Opt.
166 Generic data file
167 -ip pdo-files.dat Input, Opt.
169 Generic data file
170 -o profile.xvg Output
172 xvgr/xmgr file
173 -hist histo.xvg Output
175 xvgr/xmgr file
176 -bsres bsResult.xvg Output, Opt.
178 xvgr/xmgr file
179 -bsprof bsProfs.xvg Output, Opt.
181 xvgr/xmgr file
182 -tab umb-pot.dat Input, Opt.
184 Generic data file
185 -wcorr cycl-corr.xvg Input, Opt.
187 xvgr/xmgr file
188
191 -[no]hno
192 Print help info and quit
193 -[no]versionno
195 Print version info and quit
196 -nice int 19
198 Set the nicelevel
199 -xvg enum xmgrace
201 xvg plot formatting: xmgrace, xmgr or none
202 -min real 0
204 Minimum coordinate in profile
205 -max real 0
207 Maximum coordinate in profile
208 -[no]autoyes
210 determine min and max automatically
211 -bins int 200
213 Number of bins in profile
214 -temp real 298
216 Temperature
217 -tol real 1e-06
219 Tolerance
220 -[no]vno
222 verbose mode
223 -b real 50
225 first time to analyse (ps)
226 -e real 1e+20
228 last time to analyse (ps)
229 -dt real 0
231 Analyse only every dt ps
232 -[no]histonlyno
234 Write histograms and exit
235 -[no]boundsonlyno
237 Determine min and max and exit (with -auto)
238 -[no]logyes
240 Calculate the log of the profile before printing
241 -unit enum kJ
243 energy unit in case of log output: kJ, kCal or kT
244 -zprof0 real 0
246 Define profile to 0.0 at this position (with -log)
247 -cycl enum no
249 Create cyclic/periodic profile. Assumes min and max are the same
250 point.: no, yes or weighted
251 -alpha real 2
253 for '-cycl weighted', set parameter alpha
254 -[no]flipno
256 Combine halves of profile (not supported)
257 -[no]hist-eqno
259 Enforce equal weight for all histograms. (Non-Weighed-HAM)
260 -nBootstrap int 0
262 nr of bootstraps to estimate statistical uncertainty
263 -bs-dt real 0
265 timestep for synthetic bootstrap histograms (ps). Ensure independent
266 data points!
267 -bs-seed int -1
269 seed for bootstrapping. (-1 = use time)
270 -[no]histbsyes
272 In bootstrapping, consider complete histograms as one data point.
273 Accounts better for long autocorrelations.
274 -histbs-block int 8
276 when mixin histograms only mix within blocks of -histBS_block.
277 -[no]vbsno
279 verbose bootstrapping. Print the cummulants and a histogram file for
280 each bootstrap.
281
284 gromacs(7)
285 More information about GROMACS is available at <http://www.gro‐
287 macs.org/>.
288 Thu 26 Aug 2010 g_wham(1)