Re: [gmx-users] WHAM with multiple force constants
On 2/10/11 Feb 10,6:08 AM, jk...@ifr88.cnrs-mrs.fr wrote: Hi, I'm running an Umbrella Sampling analysis, with 1A steps in the reaction coordinate (distance) to estimate a PMF. However, owing to (high?) energetic barriers between my two proteins, some coordinates are not sampled. I intend to run simulations with stronger force constants to prevent my protein from fleeing to the nearest energetic minima. So my question is : does using different force constants to restrain the distance between my two proteins influences the PMF estimated by g_wham ? No, it is perfectly fine (and sometimes necessary) to combine umbrella simulations with different force constants. The g_wham result should be fine (if not, tell me, thanks!). Cheers, Jochen From what I understood, it doesn't seems so, as long as the distributions are well overlapped. But since I intend to invest a considerable amount of CPU time, a confirmation would be really apreciated ! Thanks, Jonathan. -- Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs-mrs.fr). -- --- 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] WHAM with multiple force constants
On Feb 10, 2011, at 3:08 PM, jk...@ifr88.cnrs-mrs.fr wrote: Hi, I'm running an Umbrella Sampling analysis, with 1A steps in the reaction coordinate (distance) to estimate a PMF. However, owing to (high?) energetic barriers between my two proteins, some coordinates are not sampled. I intend to run simulations with stronger force constants to prevent my protein from fleeing to the nearest energetic minima. So my question is : does using different force constants to restrain the distance between my two proteins influences the PMF estimated by g_wham ? No it does not assuming each window is equilibrated. From what I understood, it doesn't seems so, as long as the distributions are well overlapped. But since I intend to invest a considerable amount of CPU time, a confirmation would be really apreciated ! Thanks, Jonathan. -- Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs- mrs.fr). -- 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 thewww 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
