[gmx-users] g_wham and PMF problem

Sudha Mani Karra karra.md at gmail.com
Tue Jul 3 17:08:33 CEST 2007

Hi Mark,
         when I give only one file in the input for g_wham,

g_wham -o pmf.xvg -hist pull1.pdo ,

It asks me to give a series of inputs.The error which I get is
    :-)  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

Program g_wham, VERSION 3.3.1
Source code file: gmx_wham.c, line: 314

Fatal error:
You need to specify a series of pdo files as input

Appreciate your help.Thanks,

On 7/3/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > 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 -h suggests that -hist won't accept multiple input files. Only a
> few GROMACS utilities will do magic concatenation for you. Have a look at
> the file format and see what you need to do with a text editor or command
> line tools.
> > 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
> > -------------------------------------------------------
> Does g_wham -o pmf.xvg -hist pull1.pdo work?
> Mark
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