On 7/18/11 Jul 18,5:37 PM, Guido Polles wrote:
Hi everybody,
I noticed that GPU version of gromacs do not support the pull code,
hence i suppose g_wham cannot be used to extract a PMF. I would like
to just ask if somebody could suggest or give any hint about the way
to do umbrella sampling and extract a PMF without pull code, so that I
will have an idea before I start diving deeper into the issue, make
mistakes and potentially write useless code.
Thanks in advance for any advice.
Guido Polles
You may also try to use position restraints, not sure if they are
supported by the GPU version though.
Then use g_traj to get the displacements with respect to the umbrella
center and generate pdo files, which used to be the Gromacs 3 pull code
output. g_wham can read pdo files. Please check g_wham -h for a typical
pdo file header format.
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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