[gmx-users] NPT simulation problems

nicolas Dinter dinter at rc.m-kagaku.co.jp
Fri May 14 03:10:29 CEST 2004


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


-----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
> I run the NPT simulation and I had never found the box equilibrium, the
> 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 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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