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).
Gerrit
Luca Mollica wrote:
Hi,
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
calculations:
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
term.
ThanX to you all
Luca
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Luca Mollica
Dulbecco Telethon Institute
c/o DIBIT - S. Raffaele Scientific Institute
Biomolecular NMR Laboratory, 1B4
Via Olgettina 58
20132 Milano Italy
Tel: 00390226433497
Fax: 00390226434153
An expert is a man who has made all the mistakes
which can be made in a narrow field.
(Niels Bohr)
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