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.
-Justin
Thanks for your help!
Best,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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