[gmx-users] problem with npt
pragyachohan at hotmail.com
Mon Dec 17 11:54:18 CET 2007
ya i removed every water molecule that entered the bilayers. after pr should i do nvt before doing npt? i am doing position restrain also under npt.> Date: Mon, 17 Dec 2007 11:27:01 +0200> From: neamtuandrei at gmail.com> To: gmx-users at gromacs.org> Subject: Re: [gmx-users] problem with npt> > Hi,> have you checked if there is no water inside the membrane after the> use of genbox?> > On Dec 16, 2007 1:35 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:> > pragya chohan wrote:> > >> > > 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.> >> > Usually NVT to get the temperature right before relaxing to NPT to let> > the density equilibrate can be good idea. Look at how much your box> > changed size during your NPT to see if this effect is causing problems.> >> >> > 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> >> _______________________________________________> 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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