[gmx-users] Pressure Coupling Problem

Joe Joe ilchorny at gmail.com
Thu Apr 9 15:50:51 CEST 2009

On Thu, Apr 9, 2009 at 6:36 AM, Justin A. Lemkul <jalemkul at 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?


> 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.
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