Re: [gmx-users] g_msd = The MSD and periodic boundary condition
On Tue, Nov 24, 2009 at 1:09 PM, Omer Markovitch omer...@gmail.com wrote: On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin chihying2...@gmail.com wrote: So, how can I remove the periodic boundary condition to get the truly movement of the atoms between the two time steps ? Removing PBC and placing atoms back into their true location is easy. In general, if an atom has moved more than half of the box between two consecutive timesteps then it has jumped over the box. You can see for example eq. 19 20 in doi:10.1063/1.2968608 . --Omer. Hi, Removing periodicity from the trajectory can be done after simulation using g_traj with the -nojump option. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com -- 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] g_msd = The MSD and periodic boundary condition
Hi, Removing periodicity from the trajectory can be done after simulation using g_traj with the -nojump option. Actually, trjconv -pbc nojump Cheers, Tsjerk Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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] g_msd = The MSD and periodic boundary condition
On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin chihying2...@gmail.com wrote: So, how can I remove the periodic boundary condition to get the truly movement of the atoms between the two time steps ? Removing PBC and placing atoms back into their true location is easy. In general, if an atom has moved more than half of the box between two consecutive timesteps then it has jumped over the box. You can see for example eq. 19 20 in doi:10.1063/1.2968608 . --Omer. -- 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] g_msd = The MSD and periodic boundary condition
Hi With the periodic boundary condition, all the recorded coordinates of the atom are within the simulation box. To calculate the MSD, the movement of the center mass of the molecules between this time step with the next time step is calculated without considering the periodic boundary condition. But all the recorded coordinates of the atom are within the simulation box after considering the periodic boundary condition. Does g_msd remove the effect of the periodic boundary condition ? So, how can I remove the periodic boundary condition to get the truly movement of the atoms between the two time steps ? Thank you Lin -- 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] g_msd = The MSD and periodic boundary condition
Chih-Ying Lin wrote: Hi With the periodic boundary condition, all the recorded coordinates of the atom are within the simulation box. To calculate the MSD, the movement of the center mass of the molecules between this time step with the next time step is calculated without considering the periodic boundary condition. But all the recorded coordinates of the atom are within the simulation box after considering the periodic boundary condition. Does g_msd remove the effect of the periodic boundary condition ? Yes. So, how can I remove the periodic boundary condition to get the truly movement of the atoms between the two time steps ? Thank you Lin No need. See above. -Justin -- 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
