[gmx-users] NPT simulation problems

[nicolas Dinter]

David,

It must have a mistake on the mdrun input file but where?
thanks.

Nicolas

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org]On Behalf Of David van der Spoel
Sent: jeudi 13 mai 2004 17:22
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] NPT simulation problems


On Thu, 2004-05-13 at 05:39, nicolas Dinter wrote:
> Dear Gromacs users,
>
> I am trying to make a NPT MD simulation with 150 Benzenemethanethiol,
> alfa-methyl molecules in a 30*30*30 box. After having found the
equilibrium,
> I run the NPT simulation and I had never found the box equilibrium, the
size
> is always decreasing, also after a 300 ps simulation!
> Maybe the force field parameters are incorrect or the tau_p and tau_t are
> not well choosen (parameters witch I dont understand how to fit them).
> If somebody could help me it will be very nice. Thank you.
Check the density from g_energy and compare to experimental value. Do
also check energy and pressure.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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