[gmx-users] The energy conservation of NVE system in Gromos96

[David]

On Fri, 2005-09-30 at 15:58 -0700, Tanping Li wrote:
> Thank you for the reply. Your advice should work. But
> we need to run a lot of trajectories and do the
> average. So is there any more efficient way?
Yes, start by using PME. 
Other source of error include:
constraints - increase LINCS order to 8 an LINCS iter to 2, alt.,
decrease SHAKE tol to 1e-6 (for lower you need double precision)
Temperature/Pressure coupling ruin energy conservation, however you can
not always turn them off

> 
> Tanping
> 
> --- Nguyen Hoang Phuong
> <phuong at theochem.uni-frankfurt.de> wrote:
> 
> > 
> > > Dear all,
> > >
> > > I am simulating the hyrdation issume of protein
> > under
> > > NVE  condition. We use Gromos96 force field. But
> > the
> > > energy coservation is poor. The parameter I used
> > is:
> > >
> > >
> > > dt       =0.002
> > > rlist    =0.9
> > > rcoulomb =0.9 (pme)
> > > rvdw     =1.4 (cutoff)
> > > nstlist  =10
> > >
> > > Do you have any suggestion? Any suggestion will be
> > > appretiated greatly. Thank you very much.
> > use smaller dt, say 0.0002 and increase rcoulomb =
> > 1.4
> > 
> > Phuong
> > 
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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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