[gmx-users] problem with npt

[pragya chohan]

i started with the lipid coordinates from peter tieleman and removed the water. then i added water by genbox.
I did energy minimization followed by position restrain, which I removed gradually. all of it was done under npt. I carried out npt for 250 ps. During the next 250 ps npt run the bilayers separated and deformed. > Date: Sat, 15 Dec 2007 09:53:06 -0500> From: jalemkul at vt.edu> To: gmx-users at gromacs.org> Subject: RE: [gmx-users] problem with npt> > Quoting pragya chohan <pragyachohan at hotmail.com>:> > >> >> > I wrote yes to generate velocity. Can that be a reason for the problem? Since> > I am doing membrane simulation it is advised to do production runs in npt> > thats the only other difference.> > I think what Mark was asking for was a bit more detail on how you put your> system together. It would be helpful to know (step by step) what you did, as> that may highlight a problem. Also, what do you define as "deformed very> much?" Some fluctuations are to be expected, and 250 ps is a relatively short> time frame. In some of my bilayer simulations, the lipids look quite strange> under NVT, but after a nanosecond or two or NPT they even out and behave> normally.> > -Justin> > > ----------------------------------------> > > Date: Sat, 15 Dec 2007 06:03:27 +1100> > > From: Mark.Abraham at anu.edu.au> > > To: gmx-users at gromacs.org> > > Subject: Re: [gmx-users] problem with npt> > >> > > pragya chohan wrote:> > > >> > > > thanks for your help.> > > > My system ran fine for 250 ps but later the bilayer deformed very much.> > >> > > What was your system preparation protocol - i.e. minimization and> > > equilibration? See> > > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation> > >> > > Mark> > > _______________________________________________> > > gmx-users mailing list gmx-users at 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-request at gromacs.org.> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> >> > _________________________________________________________________> > Post free property ads on Yello Classifieds now! www.yello.in> >> http://ss1.richmedia.in/recurl.asp?pid=220_______________________________________________> > gmx-users mailing list gmx-users at 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-request at gromacs.org.> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> >> > > > ========================================> > Justin A. Lemkul> Graduate Research Assistant> 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 at 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-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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