Re: [gmx-users] How to calculate PMF after AFM pulling
huifang liu wrote: Hi Justin, Thank you for your reply, but i am still a little confused. You said in principal I should be able to extract a potential of mean force from an AFM run by simply integrating the average force along the reaction coordinate and if I have the average force as a function of position, I could simply integrate that to get the PMF. However, actually, i don't I didn't say that. The post I pointed you to did :) know how i can get the average force as a function of position and apply them in the PMF calculation. Could you give me some suggestion? Your .pdo file should have the forces, if I remember the old (3.3.x, right?) file format correctly. Then something like g_traj can extract coordinates from your trajectory. Also a good reference (and there is a ton of stuff in the list archive about this, hint): http://www.gromacs.org/pipermail/gmx-users/2002-August/002241.html I've not tried to do PMF analysis this way. It is much easier under 4.0 now to use umbrella sampling since g_wham now works. It was non-functional (or buggy at best) in previous versions. -Justin Thanks a lot. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com mailto:huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to calculate PMF after AFM pulling
huifang liu wrote: Hello everybody, I have recently run a SMD with AFM method, and i got the .pdo file. But i don't know how to use the .pdo file to calculate the PMF profile. Could someone give me some suggestion? Thanks a lot. g_wham -h -Justin Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com mailto:huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to calculate PMF after AFM pulling
Hello, Justin As the mannul said, it is intended to analyze .pdo files generated by mdrun using umbrella sampling tocreate a potential of mean force (PMF). But i were using AFM method not umbrella sampling. How can i do that? Thanks. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How to calculate PMF after AFM pulling
Hello everybody, I have recently run a SMD with AFM method, and i got the .pdo file. But i don't know how to use the .pdo file to calculate the PMF profile. Could someone give me some suggestion? Thanks a lot. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
