Re: [gmx-users] RMS deviation after position restraint dynamics
A restraint is not a constraint, and assuming that you are simulating your system at a finite temperature, you should expect to see some fluctuations in a given atom's position. Josh On May 17, 2009, at 11:47 PM, sukesh chandra gain wrote: Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little). Could you please explain why is the deviation? Thank You, Regards, Sukesh ___ 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 -- Joshua L. Adelman Biophysics Graduate Group Lab: 510.643.2159 218 Wellman HallFax: 510.642.7428 University of California, Berkeley http://nature.berkeley.edu/~jadelman Berkeley, CA 94720 USA jadel...@berkeley.edu -- ___ 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] RMS deviation after position restraint dynamics
sukesh chandra gain wrote: Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little). Could you please explain why is the deviation? You should read in the manual about how position restraints are implemented. If you wanted zero RMS deviation in one of your observables, perhaps you should re-think why you are running *dynamics*. :-) Mark ___ 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] RMS deviation after position restraint dynamics
Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little). Could you please explain why is the deviation? Thank You, Regards, Sukesh ___ 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
