On Thu, Apr 9, 2009 at 6:36 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Joe Joe wrote: > >> 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 10^2, 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. >> >> > This seems truly bizarre. How are you measuring the density (g_density, > g_energy, etc)? Both g_energy and g_density. > What are your box dimensions doing? To get that kind of sudden change in > density, your box dimensions would have to expand astronomically? Yep. > > > It's also curious that your 425K-atom system only has a PE on the order of > 10^5; my systems with 100K-200K have around 10^6 - 10^7; are you sure the > minimization is reasonable, and you are not simply seeing the effects of the > classic "blowing up" problem? If that was the case would not the NVT also not behave stably? I also agree that 10^5 seems to high. Most of that should come from water though, correct? Why would the water not relax. Maybe I should just expand the box a bit and see what happens? > What does your trajectory show? If you have multiple proteins or other > large species present, does minimization of each component individually > prior to system assembly help? I have one very large protein (antibody). I did do a gas phase minimization of the protein prior to solvation and it does not help.
_______________________________________________ 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
