Thanks for your reply. How would I know that when I get close to the equilibration state? By Pressure, Temperature,or RMSD plots?
Thanks in advance for your suggestions. Sincerely, Shima ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Monday, February 4, 2013 11:37 PM Subject: Re: [gmx-users] system far from the equilibration state On 2/4/13 2:04 PM, Shima Arasteh wrote: > Hi, > > I am simulating a system of peptide/membrane/water. If my system is far from > the equilibration, would that be correct if I use Berendsen pressure coupling > for nano seconds to do NPT equilibration and then change it to > Parrinello-Rahman to get the true pressure? Anybody may suggest me please? > Sounds reasonable. Berendsen is a useful method in such cases. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
