Re: [gmx-users] GPUs and umbrella sampling
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 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GPUs and umbrella sampling
Yes, include the harmonic restrain(s) directly into the topology. Then you may convert the info (distance(s), angle(s)) into the g_wham format (which I do not know but should be reasonably easy) or use another script to get your PMF or make you own ... it is possible. On Jul 18, 2011, at 9:37 AM, 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
