[gmx-users] g_wham: "Pull geometry direction_periodic not supported"

Jochen Hub jochen at xray.bmc.uu.se
Thu Oct 14 15:34:59 CEST 2010

  On 9/18/10 Sep 18,10:17 PM, Jochen Hub wrote:
> On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote:
>> Hi gmx-users
>> I finished a series of pulling runs using the "periodic_direction" 
>> option
>> and when I run the g_wham analysis I received the following message.
>> -------------------------------------------------------
>> Program g_wham, VERSION 4.5
>> Source code file: gmx_wham.c, line: 1369
>> Fatal error:
>> Pull geometry direction_periodic not supported
>> For more information and tips for troubleshooting, please check the 
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> Is there any way to circumvent this or should I redo all my 
>> simulations with the
>> option of "direction" instead "direction_periodic"?
> Hi Eudes,
> the g_wham has not been properly updated to gmx 4.5 yet. I'll do that 
> as soon as possible. For now, I would recommend to use g_traj to write 
> the coordinates of your pull group and your reference group and to 
> write a script that writes pdo files. Check g_wham -h to see a typical 
> pdo header. Then use g_wham -ip to compute your PMFs.

Hi Eudes,

the latest g_wham is now in (at least in the git version of) gromacs 
4.5x. For your geometry, you'll have to write the pull forces (pullf.xvg 
files) and read those into g_wham with -if. g_wham cannot read the pullx 
files written by geometry "direction_periodic" or "direction".

Please let me know it if g_wham makes any more trouble.



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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