[gmx-users] g_wham and PMF problem

[Lu Lanyuan]

I just zipped alll the *.pdo files seperately and listed them all when 
using g_wham. It's like g_wham <options> pull1.pdo.gz pull2.pdo.gz ... In 
the old gromacs versions like 3.1.4, the g_wham was broken and I was using 
a version modifined by David Bostick. You can search the mailing list for 
that information. I'm not sure whether the old problem of g_wham was fixed 
in 3.3.1.
Lanyuan Lu


>From: "Sudha Mani Karra" <karra.md at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] g_wham and PMF problem
>Date: Tue, 3 Jul 2007 10:08:33 -0500
>
>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,
>SK
>
>
>
>
>
>
>
>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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>>


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