[gmx-users] GPUs and umbrella sampling

[Jochen Hub]

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

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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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