[gmx-users] g_wham and PMF problem

Sudha Mani Karra karra.md at gmail.com
Tue Jul 3 06:30:39 CEST 2007

Hey Mark,
          Appreciate your immediate response.You can find the input and the
error below:
g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo pull5.pdo

                                :-)  g_wham  (-:

Option     Filename  Type         Description
  -o        pmf.xvg  Output       xvgr/xmgr file
-hist pull1.pdo.xvg  Output       xvgr/xmgr file

      Option   Type  Value  Description
      -[no]h   bool     no  Print help info and quit
       -nice    int      0  Set the nicelevel
      -[no]w   bool     no  View output xvg, xpm, eps and pdb files
   -[no]xvgr   bool    yes  Add specific codes (legends etc.) in the output
                            xvg files for the xmgrace program
        -min   real      0  Minimum coordinate in profile
        -max   real      0  Maximum coordinate in profile
       -bins    int    100  Number of bins in profile
   -[no]prof   bool    yes  Only calculate min and max
       -temp   real    298  Temperature
   -[no]flip   bool     no  Combine halves of profile
        -tol   real   0.01  Tolerance

Opening file pull2.pdo.

gunzip: stdin: not in gzip format
Program g_wham, VERSION 3.3.1
Source code file: gmx_wham.c, line: 90

Fatal error:
This does not appear to be a valid pdo file

Thanks ,

On 7/2/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Hey All,
> >     I am trying to use g_wham command to compute PMF.Can anyone please
> let
> > me know how to use that command?
> Well there's g_wham -h and the section on WHAMin the manual...
> > When I try giving the input files sequentially like
> >
> > g_wham -o PMF.XVG -hist pull1.pdo pull2.pdo pull3.pdo,
> >
> >  there is an error message saying, that it is not a valid input file
> > format.
> Please be specific about the error message and the file that caused it.
> Computers are precise, and you should be also in describing their
> responses to your inputs.
> Mark
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