[gmx-users] Zero Potential of Mean Force with g_wham

Jochen Hub jochen at xray.bmc.uu.se
Tue Mar 15 23:31:50 CET 2011


please use g_wham 4.5.2 or later. We largely updated g_wham recently. If 
you get a flat PMF, check the warnings that g_wham gives you and --very 
important-- look at the histograms. That usually gives you a clue where 
the histograms to not overlap.

In case you find a bug, please let me know. Otherwise, I have computed 
hundreds of PMFs with g_wham and it always worked fine.



On 3/9/11 Mar 9,11:08 PM, chris.neale at utoronto.ca wrote:
> g_wham is not the only version of wham. Try using alan grossfield's 
> version. Too often, I am afraid, gromacs accessory programs get broken 
> in an update (not sure what the general solution is here beyond 
> renewed calls for a proper test suite. Perhaps having 20+ programs is 
> not ideal for a single software suite where the real focus is only on 
> mdrun and grompp?)
> Chris.
> -- original message --
> Hi,
> I ran  g_wham 4.5.2 and did get a non-zero PMF curve.
> I assume that there is something going on with g_wham on version 4.5.1.
> Thank you for your help.
> Susana
> On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham <Mark.Abraham at 
> anu.edu.au>wrote:

Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755

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