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 <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
