Thank you Justin.
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Cc: Sent: Saturday, October 6, 2012 1:26 PM Subject: Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation On 10/6/12 3:15 AM, Shima Arasteh wrote: > > > In my own, I want to simulate POPC-water and then insert a protein in it. >Then run a new simulation for my new system. > I got the starting structure from Prof.Klauda website. Then dear Peter > provides this link to get some useful files: > http://uab.hyperfine.info/~pcl/files/popc36/ > Regarding to the pblished paper, written by Peter, NPT equilibration had been > done. I also followed them and did the NPT. But now, I'm wondering when NPT > is needed to be done and when NPT & NVT are both needed? > As long as the system is stable and you obtain converged observables, then there's nothing wrong with doing NPT as your only equilibration. Not all systems are very well behaved and do require NVT first before switching on pressure coupling, so it is often advisable. There are no hard and fast rules for equilibration, however. Every system is different, so a universal recipe is not really possible. If your method worked, then you're fine. -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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
