[gmx-users] Exclusion in PME

Janne Hirvi janne.hirvi at joensuu.fi
Fri Nov 4 09:23:08 CET 2005


I have simulated liquid droplets (L) on frozen surfaces (S) using PME method.
Interactions among frozen surface atoms have been excluded. This means that in
real space there are L-L and L-S interactions and in reciprocal space L-L, L-S,
and S-S interactions (interactions cant be excluded in reciprocal space).
Sounds a little bit strange method, but later I have calculated S-S reciprocal
energy without liquid droplet and subtracted this from the energy of the whole
system. This all because I didnt want to see really large S-S Lennard-Jones and
short range Coulombic energies. Later I noticed that I could have used
energygrps to separate all interactions...

I think this however should be just OK...am I right?   

Furthermore I would like to have comments about using 3dc correction term in
this case with or without S-S exclusion?

Thanks for any help or comments! 


Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi

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