Nope not an A/nm problem. As a simple test I take spc.gro from share/top. I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o water_center.
I then solvate with genbox, minimize and run using the mdp file I provided earlier. No matter how much minimization I do the volume of the box expands when run it using berendsen pressure coupling with a tau_p -f .1. Ilya On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale <chris.ne...@utoronto.ca>wrote: > So your problem with the small water box was solved simply by adding more > minimization? I then suspect that all of your problems are simply related to > a bad starting structure -- and by the sound of it is really is very bad. > Are you sure that you don't have an angstrom / nm problem here? > > Chris. > > -- original message -- > > So I got my small water box (800 waters) to behave stably with pressure > coupling after more minimization but I still can't get my large system to > work with pressure coupling. I tried minimizing but I can never get the > Fmax > to be less 102, which is pretty normal for protein/water simulations of > large proteins, at least from my experience. I have since run 400 ps NVT > as > the system (425K atoms) is quite stable. The <P.E.> is 2E-05. Since I am > using 4fs time steps gromacs won't let me use a tau_p less than .4. Not > sure > what else to do except run NVT, which is what I was going to do after I got > the density equilibrated. BTW, I am using octahedral PBC, but that should > not make a difference with respect to P coupling, should it? Below is my > whole mdp file. As a reminder my density in the system goes from 1.0 - .1 > in > 10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the > amount of time it takes for my system to expand increases but it still > expands. > > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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