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

[Gerrit Groenhof (RUG)]

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
>
>
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>
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>
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