Gavin Melaugh wrote:
Hi all
I have set up a simulation with PBC using PME and specify an energy
group enclusion involving some virtual sites and a hydrocarbon chain.
i.e. hydrocarbon chain is one energy group and the virtual sites
constitute the other group. Grompp generates the following warning
"Can not exclude the lattice Coulomb energy between energy groups"
I have checked the mailing list and the manual but there doesn't seem to
be any concise answers. Given the fact that both groups are not charged
is it O.K. to ignore this warning.
Probably. The warning indicates that one cannot use energygrp_excl to exclude
components of the PME mesh; such exclusions only apply to short-range
interactions that can be decomposed pairwise. Since the PME mesh is dependent
on all the entities in the system, there is not way to simply calculate the
mesh, except for some interactions between groups A and B. If there are no
charges on groups A and B, you should be fine.
-Justin
--
========================================
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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