[gmx-users] Electrostatics & LJ params

[Nuno R. L. Ferreira]

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?


NUno

P.S. running gmx3.1.4
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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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