[gmx-users] profiles az a function of z
Hello, In a simulation, how is it possible to extract the profiles e.g. potential as a function of z (coordinate axis of box)? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] profiles az a function of z
Paymon Pirzadeh wrote: Hello, In a simulation, how is it possible to extract the profiles e.g. potential as a function of z (coordinate axis of box)? g_potential can do this for electrostatic potential, but I don't know about anything else. I don't think it is a trivial question to decompose the potential of the entire system along any axis. -Justin Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate 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://lists.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] profiles az a function of z
Well, the main purpose is to average the energy or any desired property along any desired coordinate axis. simple binning of the box will do the job, but I was wondering if this can be done in general with gromacs post simulation tools. Payman On Fri, 2009-10-16 at 16:05 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Hello, In a simulation, how is it possible to extract the profiles e.g. potential as a function of z (coordinate axis of box)? g_potential can do this for electrostatic potential, but I don't know about anything else. I don't think it is a trivial question to decompose the potential of the entire system along any axis. -Justin Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 mailing listgmx-users@gromacs.org http://lists.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] profiles az a function of z
Paymon Pirzadeh wrote: Well, the main purpose is to average the energy or any desired property along any desired coordinate axis. simple binning of the box will do the job, but I was wondering if this can be done in general with gromacs post simulation tools. No, there is no general way to do this. Individual tools might let you construct various analysis groups according to some geometric criterion, but in general you need to use atomic indices in .ndx files. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
