[gmx-users] energygrp_excl and PME
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 24 11:34:54 CEST 2006
Abil Aliev wrote:
> I have used mdp file for md runs with
> coulombtype = Cut-off
> energygrps = Protein SOL Terminal
> energygrp_excl = Terminal Terminal Terminal SOL
> freezegrps = Terminal
> freezedim = Y Y Y
> and had no warning messages on grompp-ing. But, when
> I change
> coulombtype = PME
> a warning message is issued by grompp:
> "WARNING 1 [file "stide.top", line 40]:
> Can not exclude the lattice Coulomb energy between
> energy groups"
> Is there anyway to avoid this warning by changing
> energygrp_excl or other options in the mdp file while
> keeping PME?
The file reference is not accurate, but the warning means that even if
you exclude the interaction in real space there still is an interaction
in fourier space, due to a restriction in the software.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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