[gmx-users] pressure scaling

[nicolas Dinter]

Dear Berk,

I started with a very large box and reduced it by NPT, and get equilibrium
box. But I didn't have LR interaction, so I changed rlist and get it, but
the simulation crash by the pressure scaling.

I tryied the way of Yuguang to solve it, but the problem remains, later but
still.

Do I have to rebegin all the reducing box procedure because I didn't have LR
interaction?

Nicolas

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org]On Behalf Of Berk Hess
Sent: mardi 3 août 2004 16:54
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] pressure scaling





>From: "nicolas Dinter" <dinter at rc.m-kagaku.co.jp>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] pressure scaling
>Date: Tue, 3 Aug 2004 14:51:24 +0900
>
>Dear Berk,
>
>I used a tau_p = 10, then I tried different values for compressibility:
>1st:4.5e-5 (initial crash), 14.5e-5, 0.5e-5, 0.5e-6, 0.5e-4 and 4.5e-3. But
>there isn't many changes, the cash occured allmost at the same step: 303
>(4.5e-5),291 (14.5e-5),301 (0.5e-5),301 (0.5e-6),299(0.5e-4) and 293
>(4.5e-3).
>Ok so if I undestood well the pressure scaling error occurs when the box
>enter in resonance, but normaly with low compressibility it must not occur
>or at least at different steps (more difficult to change the box) especialy
>with low pressure.

Low pressure has nothing to do with it.
For water a pressure of 500 Bar results only in a density change of 1%,
which almost does not affect the dynamics.

My guess would be that you have started from a very unequilibrated
conformation.
Have you performed energy minimization before starting MD?
Aslo you could start from a much lower density.

>
>So I would like to know which are the parameter which drive this error:
>there is the time step (I took:0.0005ps), the tau_p parameter (I took 10ps)
>and the compressibility. And what else?
>
>I still not well undestand what does represent tau_p is my draw is a
>correct
>understanding? (see atached file).

No.
If the compressibility is correct the pressure deviation decays as:
exp(-t/tau_p)

Berk.

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