Gavin Melaugh wrote:
Hi Justin
Thanks for the reply. I take it then, if I use the maxwarn option, it
will still apply the exclusion for the short-range non-bonding interactions.
Yes, that should work. The error message is only there to prevent people from
erroneously thinking they can exclude the PME mesh term.
-Justin
Cheers
Justin A. Lemkul wrote:
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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