[gmx-users] Jarzinsky's inequality from SMD simulation
Hi, I have done some steered MD simulation and I want to construct the potential of mean force from these pull-profile using Jarzinsky's inequality. I wanted to see whether, in updated version of gromacs, there is any implementation of extracting PMF from SMD simulations. If not, can anyone suggest some guidelines how to do it. Sanku-- 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] Jarzinsky's inequality from SMD simulation
There is a way to extract the PMF from sMD simulations using the weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a nice job of explaining it: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html - Laura On 10/31/2011 11:05 AM, Sanku M wrote: Hi, I have done some steered MD simulation and I want to construct the potential of mean force from these pull-profile using Jarzinsky's inequality. I wanted to see whether, in updated version of gromacs, there is any implementation of extracting PMF from SMD simulations. If not, can anyone suggest some guidelines how to do it. Sanku -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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] Jarzinsky's inequality from SMD simulation
Hi Laura, I do not think Justin Lemkul's tutorial is suggesting extracting PMF using SMD simulation. What is does that it uses SMD to generate the initial configurations for different windows and then perform umbrella sampling separately on each windows to subsequently extract the PMF using WHAM based on the data set on umbrella sampling. Sanku From: Laura Kingsley lking...@purdue.edu To: gmx-users@gromacs.org Sent: Monday, October 31, 2011 11:09 AM Subject: Re: [gmx-users] Jarzinsky's inequality from SMD simulation There is a way to extract the PMF from sMD simulations using the weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a nice job of explaining it: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html - Laura On 10/31/2011 11:05 AM, Sanku M wrote: Hi, I have done some steered MD simulation and I want to construct the potential of mean force from these pull-profile using Jarzinsky's inequality. I wanted to see whether, in updated version of gromacs, there is any implementation of extracting PMF from SMD simulations. If not, can anyone suggest some guidelines how to do it. Sanku -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing list gmx-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
Re: [gmx-users] Jarzinsky's inequality from SMD simulation
Yes, I believe that is correct. I know that this is one way to get the PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky equation explicitly to extract the PMF from just a sMD run with Gromacs. On 10/31/2011 01:29 PM, Sanku M wrote: using SMD simulation. What is does that it uses SMD to generate the initial configurations for different windows and then perform umbrella sampling separately on each windows to subsequently extract the PMF using WHAM based on the data set on umbrella sampling. -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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] Jarzinsky's inequality from SMD simulation
Laura Kingsley wrote: Yes, I believe that is correct. I know that this is one way to get the PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky equation explicitly to extract the PMF from just a sMD run with Gromacs. One approach: http://lists.gromacs.org/pipermail/gmx-users/2011-August/063477.html I've never tried it, so I don't know if that is correct or not. Go to http://www.gromacs.org/Support/Mailing_Lists/Search and search for Jarzynski and you will pull up more on this topic. -Justin On 10/31/2011 01:29 PM, Sanku M wrote: using SMD simulation. What is does that it uses SMD to generate the initial configurations for different windows and then perform umbrella sampling separately on each windows to subsequently extract the PMF using WHAM based on the data set on umbrella sampling. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
