[gmx-users] time step vs system
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 1 12:55:03 CEST 2004
On Tue, 2004-06-01 at 12:09, Nuno R. L. Ferreira wrote:
> On Tuesday 01 June 2004 11:03 am, Xavier Periole wrote:
> > Nuno R. L. Ferreira wrote:
> > >Hi there
> > >
> > >Reading some papers about simulation of bilayer systems, it seams that the
> > >max. recomended dt is about 5 fs.
> > >What about in systems with bilayer+protein?
> > >
> > >How can I know what's the max. dt for a specific system?
> > For proteins I would not recommand using bigger than 2fs. Depends in the
> > problem your are addressing. People use more thant 2fs but the problems are
> > generaly about folding or large conformational space to explore. In
> > those cases
> > the details are not that important. If your protein have to reorganize
> > or adapt
> > to a contraint I would keep a 2fs time step.
> Like a protein interacting to a bilayer surface, right?
> So I will stick to 2 .
Actually, if you use dummies you can go higher. For protein folding like
simulations I routinely use 4 fs with pdb2gmx -dummy h
This works well both with OPLS and GROMOS force fields. (Don't use
> Thank you Xavier
> > In the case of bilayers, it is more like a solvent than like a protein.
> > The interactions
> > are less sensitive thant in a protein and the properties are global and
> > not much in
> > details.
> > XAvier
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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