[gmx-users] Electrostatics & LJ params

[David van der Spoel]

On Wed, 2004-02-04 at 18:09, Nuno R. L. Ferreira wrote:
> Hi
> 
> After reading some previous messages about rlist,rvdw and rcoulomb, I got a
> bit confused (I think I'm not the only one).
> I started to do my sims under NAMD, and perhaps I misinterpreted the
> concepts during software migration 2 gmx, although the general ideas must be
> the same.
> 
> I've done some md runs (peptide+solvent) with the following params:
> 
> nstlist = 10
> coulombtype = PME ; vdwtype = shift
> rlist = 1.0
> rvdw_switch = 1.0 ; rvdw = 1.4
> rcoulomb = 1.0
> 
> 1- the full direct and reciprocal space parts are calculated each step
> 2- Lennard-Jones interactions within 1.0 nm are calculated every step, and
> long range forces out to 1.4 updated every 10 steps
> 
> Is my interpretation correct? Are there any inconsistent params?

Yes. We recommend nstlist = 5

> 
> NUno
> 
> P.S. running gmx3.1.4
> ######################################
> Nuno Ricardo Santos Loureiro da Silva Ferreira
> Departamento de Química
> Faculdade de Ciências e Tecnologia
> Universidade de Coimbra
> 3004-535 Coimbra - Portugal
> Fax: +351 239 827703  - www.biolchem.qui.uc.pt
> ########################################
> 
> 
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-- 
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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