I finally figured it out. I went through every parameter step by step and it turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs would have given me a warning (hint hint). That explains why my P.E. was 10^-5 instead of 10^-6. Thanks everyone for trying!!!. Sometime the most obvious mistake takes some time to figure out. Cheers,
Ilya On Fri, Apr 10, 2009 at 8:05 AM, <chris.ne...@utoronto.ca> wrote: > Alright, sorry that I wasn't able to help. I'm confused by some apparent > contradictions in your posts and I'm not sure that I'm going to be useful to > you here. > > Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: > "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." > > Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html: > "So I got my small water box (800 waters) to behave stably with pressure > coupling after more minimization ..." > > Good luck. > Chris. > > -- original message -- > > > 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: > > [Hide Quoted Text] > 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 ... > > _______________________________________________ > 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 thewww 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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