[gmx-users] g_wham and PMF problem

Arneh Babakhani ababakha at mccammon.ucsd.edu
Tue Jul 3 15:44:32 CEST 2007

You have to collect all of the pdo files into one directory (and so you'll
have to rename them if they all have identical names).  Then zip them
using gzip: gzip *.pdo

Then you can use the g_wham code, something like:
g_wham *.gz -bins 1000 -temp 300 -auto

>> 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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