[gmx-users] Constraint algorithm error

[nicolas Dinter]

Anton,

Seeing that it was a constraint error I ran a NPT simulation, without any
constraint (mdp-itp),
then my calcul runs for about 9.845ps (for a 10ps sim) and crash for
pressure scaling error (tau_p=10 ps, ref_p=1bar), and thus with a very small
time step (0.00001 ps)to avoid this error. But more surprizing the box size
do not change at all! Being far from the equilibrium density I am surprized.

Nicolas


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org]On Behalf Of Anton Feenstra
Sent: samedi 24 juillet 2004 00:49
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Constraint algorithm error


nicolas Dinter wrote:

> Anton,
>
> There is only the diphenyl carbonate ( Phenyl-O-CO-O-Phenyl ) in the box.
> I use the Berendsen prssure coupling with tau_p=10 (so very slow).
> I used constraints as bonds in the itp file.

Right - so you have constaints regardless of the .mdp file option set.

Now you will need to look at strange energies and/or bad contacts.
You may need to decrease nstener or nstxtcout to see the problem starting
before the simulation crashes. Also, you may need to disable the output
buffering by setting LOGBUFS=0 (environment variable).


--
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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