[gmx-users] PME

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 6 19:32:29 CEST 2011

Elisabeth wrote:
> Hello Justin,
> Several days ago you answered my question about calculating nonbonded 
> terms:
> Question: If I want to look at nonboded interactions only, do I have to 
> add  Coul. recip.  to [ LJ (SR)  + Coulomb (SR) ] ?
> Answer: The PME-related terms contain both solute-solvent, 
> solvent-solvent, and potentially solute-solute terms (depending on the 
> size and nature of the solute), so trying to interpret this term in some 
> pairwise fashion is an exercise in futility.
> my question is if I want to add up nonbonded related terms to get inter 
> molecular energies, do I have to add Coul. recip. or it is already 
> included in Coulomb (SR)? 

They are separate energy terms.  The PME mesh terms is "Coul. recip." and the 
short-range interactions (contained within rcoulomb, calculated by a modified 
switch potential) are "Coulomb (SR)."

> and also, for a A-B system, I have been using energy groups to extract  
> solute-solvent, solvent-solvent, solute-solute terms. Did you mean that 
> applying doing so with PME as electrostatics treatment is not correct?

PME has been consistently shown to be one of the most accurate long-range 
electrostatics methods and is widely used, but in your case is preventing you 
from extracting the quantity you're after (if it can even be reasonably defined 
at all).  Using energygrps will not resolve the problem I described above.  The 
"Coul. recip." term contains long-range energies between (potentially) A-B, A-A, 
and B-B, depending on the nature of what A and B are.  The only terms that are 
decomposed via energygrps are the short-range terms, which are calculated 
pairwise.  Thus, with PME, there is no straightforward way to simply define an 
"intermolecular energy" for a heterogeneous system.  You might be able to define 
such a term for a completely homogeneous system (which also assumes that the 
sampling has converged such that the charge densities etc are uniform...but I'm 
sort of thinking out loud on that), but not one that is a mixture.


> Thanks for your help!
> Best,


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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