[gmx-users] pressure scaling

Berk Hess gmx3 at hotmail.com
Tue Aug 3 09:56:47 CEST 2004

>From: "Mu Yuguang (Dr)" <YGMu at ntu.edu.sg>
>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 14:08:18 +0800
>Dear all,
>May it be some problems not related to the pressure coupling?
>Nicolas, did you try without pressure coupling, still crash ?
>I found in my simulations, some trajectories crash repetitively without 
>pressure coupling. The phenomena I found is that such crash usually happens 
>when my molecule cross the box border.
>I solved it in the following way:
>I reorganize the simulation system, by placing the solute (usually big) in 
>the center of the simulation box, using trjconv command, then the 
>simulation can go on.

In Gromacs it does not matter where you place the solute in the box.
I don't see how placing the solute in the center of the box could help.
The only thing this operation could do it slightly change the coordinates
which might avoid a crash, since the simulation will take a different
trajectory as MD is inherently chaotic.

>Such crashes do not dependent on force fields used, PME or cut-offs, I use 
>simple cubic box.
>I think maybe some bugs in the treatment of periodic conditions ??

There are no bugs in the treatment of the periodic boundary conditions.


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