Quoting Mahnam <[email protected]>: > > > In God We Trust > Hello Dear GMX users > We would like to perform MD simulation of a protein in attendance of > biomembrane (POPE). On the basis of Kalp tutorial, can we combine position > restraints and NPT equlibration in one phase?. We attached NPT.mdp in this > mail. Please guide us.
In the tutorial, position restraints are applied during both NVT and NPT equilibration, with the purpose of separately equilibrating temperature and pressure. You could try to do both in one NPT run, but in my experience, POPE requires some finesse during equilibration, so two phases are probably best. -Justin > Many thanks in advance for your help and your reply. > Yours truly > Karim Mahnam > Institute of Biochemistry and Biophysics (IBB) > Tehran University > P.O.box 13145-1384 > Tehran > Iran > http://www.ibb.ut.ac.ir/ > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [email protected] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
