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
