Provided by: gromacs-data_4.6.5-1build1_all bug


       g_wham - weighted histogram analysis after umbrella sampling

       VERSION 4.6.5


       g_wham  -ix  pullx-files.dat  -if  pullf-files.dat  -it tpr-files.dat -ip pdo-files.dat -o
       profile.xvg -hist histo.xvg -oiact iact.xvg -iiact iact-in.dat -bsres bsResult.xvg -bsprof
       bsProfs.xvg  -tab  umb-pot.dat -[no]h -[no]version -nice int -xvg enum -min real -max real
       -[no]auto -bins int -temp real -tol real -[no]v -b real -e  real  -dt  real  -[no]histonly
       -[no]boundsonly  -[no]log  -unit  enum -zprof0 real -[no]cycl -[no]sym -[no]ac -acsig real
       -ac-trestart real -nBootstrap int -bs-method enum -bs-tau real -bs-seed int  -histbs-block
       int -[no]vbs


       This is an analysis program that implements the Weighted Histogram Analysis Method (WHAM).
       It is intended to analyze output files  generated  by  umbrella  sampling  simulations  to
       compute a potential of mean force (PMF).

       At present, three input modes are supported.

         *  With  option   -it,  the  user  provides a file which contains the  file names of the
       umbrella simulation run-input files ( .tpr files),  AND, with option  -ix,  a  file  which
       contains  file names of  the pullx  mdrun output files. The  .tpr and pullx files must  be
       in corresponding order, i.e. the first  .tpr created the  first pullx, etc.

        * Same as the previous input mode, except that the the user    provides  the  pull  force
       output file names ( pullf.xvg) with option  -if.   From the pull force the position in the
       umbrella potential is  computed. This does not work with tabulated umbrella potentials.
        * With option  -ip, the user provides file names of (gzipped)  .pdo  files,  i.e.     the
       GROMACS  3.3  umbrella  output files. If you have some unusual reaction coordinate you may
       also generate your own  .pdo files and  feed them with the  -ip option  into  to   g_wham.
       The  .pdo file header  must be similar to the following:

         UMBRELLA      3.0

        Component selection: 0 0 1

        nSkip 1

        Ref. Group 'TestAtom'

        Nr. of pull groups 2

        Group 1 'GR1'  Umb. Pos. 5.0 Umb. Cons. 1000.0

        Group 2 'GR2'  Umb. Pos. 2.0 Umb. Cons. 500.0

       The  number of pull groups, umbrella positions, force constants, and names may (of course)
       differ. Following the header, a time column and a data column for each pull group  follows
       (i.e.  the  displacement  with respect to the umbrella center). Up to four pull groups are
       possible per  .pdo file at present.

       By default, the output files are

          -o      PMF output file

          -hist   Histograms output file

       Always check whether the histograms sufficiently overlap.

       The umbrella potential is assumed to be harmonic and the force constants are read from the
       .tpr  or   .pdo  files. If a non-harmonic umbrella force was applied a tabulated potential
       can be provided with  -tab.

       WHAM OPTIONS ------------

          -bins   Number of bins used in analysis

          -temp   Temperature in the simulations

          -tol    Stop iteration if profile (probability) changed less than tolerance

          -auto   Automatic determination of boundaries

          -min,-max   Boundaries of the profile

       The data points that are used to compute the profile can be restricted with  options   -b,
       -e, and  -dt.  Adjust  -b to ensure sufficient equilibration in each umbrella window.

       With   -log  (default) the profile is written in energy units, otherwise (with  -nolog) as
       probability. The unit can be specified with  -unit.  With energy output, the energy in the
       first  bin  is defined to be zero.  If you want the free energy at a different position to
       be zero, set  -zprof0 (useful with bootstrapping, see below).

       For cyclic or periodic reaction coordinates (dihedral angle, channel PMF  without  osmotic
       gradient),  the  option   -cycl is useful.  g_wham will make use of the periodicity of the
       system and generate a periodic PMF. The first and the last bin of the reaction  coordinate
       will assumed be be neighbors.

       Option   -sym  symmetrizes  the profile around z=0 before output, which may be useful for,
       e.g. membranes.

       AUTOCORRELATIONS ----------------

       With  -ac,  g_wham estimates the integrated  autocorrelation  time  (IACT)  tau  for  each
       umbrella  window  and  weights  the  respective  window with 1/[1+2*tau/dt]. The IACTs are
       written to the file defined with  -oiact. In verbose mode, all  autocorrelation  functions
       (ACFs)   are   written   to    hist_autocorr.xvg.   Because  the  IACTs  can  be  severely
       underestimated in case of limited sampling, option  -acsig allows one to smooth the  IACTs
       along  the reaction coordinate with a Gaussian (sigma provided with  -acsig, see output in
       iact.xvg). Note that the IACTs are estimated by simple integration of the ACFs  while  the
       ACFs  are  larger  0.05.   If you prefer to compute the IACTs by a more sophisticated (but
       possibly less robust) method such as fitting to a double exponential, you can compute  the
       IACTs  with   g_analyze  and  provide  them  to  g_wham with the file  iact-in.dat (option
       -iiact), which should contain one line per input file ( .pdo  or  pullx/f  file)  and  one
       column per pull group in the respective file.

       ERROR ANALYSIS --------------

       Statistical  errors  may be estimated with bootstrap analysis. Use it with care, otherwise
       the statistical error may be substantially underestimated.  More background  and  examples
       for  the  bootstrap technique can be found in Hub, de Groot and Van der Spoel, JCTC (2010)
       6: 3713-3720.

        -nBootstrap defines the number  of  bootstraps  (use,  e.g.,  100).   Four  bootstrapping
       methods are supported and selected with  -bs-method.

          (1)   b-hist    Default: complete histograms are considered as independent data points,
       and the bootstrap is carried out by assigning random weights to the histograms  ("Bayesian
       bootstrap").  Note  that  each  point  along  the  reaction  coordinate must be covered by
       multiple independent histograms (e.g. 10 histograms), otherwise the statistical  error  is

          (2)   hist     Complete histograms are considered as independent data points.  For each
       bootstrap, N histograms  are  randomly  chosen  from  the  N  given  histograms  (allowing
       duplication,  i.e.  sampling  with  replacement).   To  avoid  gaps without data along the
       reaction coordinate blocks of histograms ( -histbs-block) may be defined.  In  that  case,
       the  given  histograms  are  divided into blocks and only histograms within each block are
       mixed. Note that the histograms within each block must be representative for all  possible
       histograms, otherwise the statistical error is underestimated.

          (3)  traj  The given histograms are used to generate new random trajectories, such that
       the generated data points are distributed according  the  given  histograms  and  properly
       autocorrelated.  The autocorrelation time (ACT) for each window must be known, so use  -ac
       or provide the ACT with  -iiact. If the ACT of all windows are identical (and known),  you
       can also provide them with  -bs-tau.  Note that this method may severely underestimate the
       error in case of limited sampling, that is if individual histograms do not  represent  the
       complete phase space at the respective positions.

          (4)   traj-gauss   The  same as method  traj, but the trajectories are not bootstrapped
       from the umbrella histograms but from Gaussians with the average and width of the umbrella
       histograms. That method yields similar error estimates like method  traj.

       Bootstrapping output:

          -bsres   Average profile and standard deviations

          -bsprof  All bootstrapping profiles

       With   -vbs  (verbose  bootstrapping),  the histograms of each bootstrap are written, and,
       with bootstrap method  traj, the cumulative distribution functions of the histograms.


       -ix pullx-files.dat Input, Opt.
        Generic data file

       -if pullf-files.dat Input, Opt.
        Generic data file

       -it tpr-files.dat Input, Opt.
        Generic data file

       -ip pdo-files.dat Input, Opt.
        Generic data file

       -o profile.xvg Output
        xvgr/xmgr file

       -hist histo.xvg Output
        xvgr/xmgr file

       -oiact iact.xvg Output, Opt.
        xvgr/xmgr file

       -iiact iact-in.dat Input, Opt.
        Generic data file

       -bsres bsResult.xvg Output, Opt.
        xvgr/xmgr file

       -bsprof bsProfs.xvg Output, Opt.
        xvgr/xmgr file

       -tab umb-pot.dat Input, Opt.
        Generic data file


        Print help info and quit

        Print version info and quit

       -nice int 19
        Set the nicelevel

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -min real 0
        Minimum coordinate in profile

       -max real 0
        Maximum coordinate in profile

        Determine min and max automatically

       -bins int 200
        Number of bins in profile

       -temp real 298

       -tol real 1e-06

        Verbose mode

       -b real 50
        First time to analyse (ps)

       -e real 1e+20
        Last time to analyse (ps)

       -dt real 0
        Analyse only every dt ps

        Write histograms and exit

        Determine min and max and exit (with  -auto)

        Calculate the log of the profile before printing

       -unit enum kJ
        Energy unit in case of log output:  kJ,  kCal or  kT

       -zprof0 real 0
        Define profile to 0.0 at this position (with  -log)

        Create cyclic/periodic profile. Assumes min and max are the same point.

        Symmetrize profile around z=0

        Calculate integrated autocorrelation times and use in wham

       -acsig real 0
        Smooth autocorrelation times along reaction coordinate with Gaussian of this sigma

       -ac-trestart real 1
        When computing autocorrelation functions, restart computing every .. (ps)

       -nBootstrap int 0
        nr of bootstraps to estimate statistical uncertainty (e.g., 200)

       -bs-method enum b-hist
        Bootstrap method:  b-hist,  hist,  traj or  traj-gauss

       -bs-tau real 0
        Autocorrelation time (ACT) assumed for all histograms. Use option  -ac if ACT is unknown.

       -bs-seed int -1
        Seed for bootstrapping. (-1 = use time)

       -histbs-block int 8
        When mixing histograms only mix within blocks of  -histbs-block.

        Verbose bootstrapping. Print the CDFs and a histogram file for each bootstrap.



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                g_wham(1)