[gmx-users] PME usage in 3.3 & g_energy: doubt ?

Luca Mollica mollica.luca at hsr.it
Tue Aug 1 16:24:44 CEST 2006


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 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

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