[gmx-users] g_wham giving flat free energy

Jochen Hub jochen at xray.bmc.uu.se
Wed Apr 28 10:39:49 CEST 2010

Michael McGovern wrote:
> Hi everyone.  I'm having some trouble using g_wham to analyze some 
> results.  I have some simulations from gromacs 3.3 using the pull 
> code.  I'm using the latest version of g_wham to analyze the results, 
> which the help file says is ok, using the -ip option.  
> I've gotten almost everything to work, and it generates histograms 
> that seem perfectly reasonable, but sometimes the free energy it 
> outputs is completely flat, with each bin having a free energy value 
> of 0.
> I've played around with the -b and -e options using only part of my 
> data, and sometimes it gives non-flat free energies, other times not. 
>  I see no logic to when it works and when it doesn't.  My data does 
> have good overlap of the histograms, and it sometimes converges even 
> when I use data that have no overlaps, so that doesn't seem to be the 
> problem.
> I'm completely confused.  Does anyone know what could cause this?

Hi Micheal,

how large is your data? Could you send me a tar.gz of your pdo files? I 
would like to make sure that there is no bug in g_wham.


Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755

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