On Fri, Apr 5, 2013 at 9:55 AM, Shima Arasteh <shima_arasteh2...@yahoo.com>wrote:
> > > Hi all, > > I am trying to simulate a system of protein and lipid bilayer ( in this > case POPC). The ff I am using is CHARMM36 and I used related settings from > literature. > > I used InflateGRO to pack the lipids around my protein. Then put a > position restraint on my protein and P atoms of POPC. With these position > restraints I ran NVT for 1ns and NPT for around10 ns. > ( I need to say that NPT has been done in three steps: 1.First 5ns with > position restraint on whole protein and P atoms > 2. Then 3 ns with position restraint on just protein atoms > 3. And finally 1 ns with position restraint on protein without H atoms. ) > In fact, I tried to prevent any crash by sudden changes. > > > Seems reasonable. > Next, I tried to run MDRUN, but I get the error of "some water molecules > can not be settled". This means that my system has not been equiliberated > sufficiently. OK, what should I do? How can I solve it? Water molecules can > not be deleted in this step because I will get another fatal error as a > result. > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > My system seems fine. The pressure and energy plots don't show anything > unusual. But I dont know how can I solve the problem. Would you please give > me any suggestions? > Reducing the timestep and also changing the thermostat could not help my > system to overcome this problem. What would be the best solution? > > Please post a complete .mdp file. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists