[gmx-users] PME usage in 3.3 & g_energy: doubt ?
Gerrit Groenhof (RUG)
g.groenhof at rug.nl
Tue Aug 1 16:17:11 CEST 2006
First, with rlist = rvdw, you will not get long range Lennard Jones
interactions. In fact I would recommend using a larger vdw cut-off, as
0.9 is very short. Are you sure you are using the same mdp file?
About the LR coulomb, it will only appear if you have rlist < rcoulomb.
In that case the sphere between rlist and rcoulomb is frozen for the
direct electrostatic interaction calculation during PME between two
nlist updates (set by nlist = X).
Luca Mollica wrote:
> having started to use GMX 3.3 since few months, I have a doubt about
> using PME treatement for electrostatics and extracting energies from
> the corresponding .edr file.
> After simulation, trying to use g_energy -f energy.edr -o Energy.xvg,
> I get the following groups:
> Mu-Y Mu-Z Coul-SR:Protein-Protein
> LJ-SR:Protein-Protein Coul-14:Protein-Protein LJ-14:Protein-Protein
> Coul-SR:Protein-SOL LJ-SR:Protein-SOL Coul-14:Protein-SOL
> LJ-14:Protein-SOL Coul-SR:Protein-Cl LJ-SR:Protein-Cl
> Coul-14:Protein-Cl LJ-14:Protein-Cl Coul-SR:SOL-SOL
> LJ-SR:SOL-SOL Coul-14:SOL-SOL LJ-14:SOL-SOL
> Coul-SR:SOL-Cl LJ-SR:SOL-Cl Coul-14:SOL-Cl
> I have notice a difference with respect to 3.2 version of GMX, that is
> the absence of LR terms for both LJ and Coulombic terms: 3.2 provides
> a LR term for PME calculations, 3.3 does not provide it.
> Now, what about the missing terms ? Considering the theory that stays
> behind the Ewald sums, the SR term should include only the real part,
> but I cannot understand quite well what I have to do with the
> 'missing' reciprocal + dipolar + self LR term ....
> Please consider that I have used the following terms for energy
> pbc = xyz
> ns_type = grid
> rlist = 0.9
> rcoulomb = 0.9
> fourierspacing = 0.12
> pme_order = 4
> rvdw = 0.9
> coulombtype = PME
> ewald_rtol = 1e-5
> which corresponds to pretty standard PME parameters .... and also,
> testing Cut Off treatement of electrostatics, I get back the LR and SR
> ThanX to you all
> Luca Mollica
> Dulbecco Telethon Institute
> c/o DIBIT - S. Raffaele Scientific Institute
> Biomolecular NMR Laboratory, 1B4
> Via Olgettina 58
> 20132 Milano Italy
> Tel: 00390226433497
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