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
GROMACS
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.
Cheers,
Jochen
--
---------------------------------------------------
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
http://xray.bmc.uu.se/~jochen/index.html
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