[gmx-users] RE: Benzene again2

[David]

On Tue, 2004-07-06 at 13:41, nicolas Dinter wrote:
> Dear David,
> 
> I used the Gromacs Force field.
> Why simulate a so long simulation?

because the MSD should converge to a straight line.


> 
> Nicolas
> 
> -----Original Message-----
> From: David [mailto:spoel at xray.bmc.uu.se]
> Sent: mardi 6 juillet 2004 20:35
> To: nicolas Dinter
> Subject: RE: Benzene again2
> 
> 
> On Tue, 2004-07-06 at 13:12, nicolas Dinter wrote:
> > David,
> >
> > After manny simulations I always get a strange msd (see atached
> file).Which
> > is half lower than the experimental data. How can I let the Benzene moving
> > like in liquid in the equilibrium state?
> Force field can be wrong. Have you tried OPLS? Also you simulate at
> least 500 ps.
> 
> Let's move this discussion to the gmx-users list, such that other people
> can profit from it as well.
> > thanks.
> >
> > Nicolas
> --
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++