[gmx-users] time step vs system

Nuno R. L. Ferreira nunolf at ci.uc.pt
Tue Jun 1 12:09:43 CEST 2004

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 .
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

Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica 
Departamento Química
Universidade de Coimbra
"Do not worry about your difficulties in maths.
 I can assure you that mine are still greater."

More information about the gromacs.org_gmx-users mailing list