[gmx-users] NPT simulation problems

[David van der Spoel]

On Fri, 2004-05-14 at 03:10, nicolas Dinter wrote:
> David,
> 
> It must have a mistake on the mdrun input file but where?
> thanks.
have you checked those results?
> 
> 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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> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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