[gmx-users] pressure scaling

nicolas Dinter dinter at rc.m-kagaku.co.jp
Tue Aug 3 11:37:29 CEST 2004

First I used constraint for bonds in the itp file, but now it's turned off.
So now there isn't any constraint in both itp and mdp file.
Conserning the topology file I checked it at least twice and I am pretty
sure that it's correct.
And tau_t = 0.1.

-----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 18:12
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] pressure scaling

>Before using this values of rvdw, rcoulomb, rlist and nstlist I had
>rcoulomb=rlist=nstlist=1.3 and only SR energies, and when I turned rlist to
>1.1 I get SR and LR energies.

But this should not have a large effect on the simulation.
Having all cut-off's at 1.3 is more accurate, but is
computationally more expensive.

Something else:
Are you using constraints?
If you use constraints you should be able to use a time step
of at least 0.002 and maybe even up to 0.005.

Many other things could be wrong.
The most probable cause is always an not well equilibrated
starting structure.
But there could also be an error in your topology.

What is your tau_t?
The coupling time for temperature bath should be a least
a factor of two smaller than tau_p.


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