Abil Aliev wrote:
Hello,
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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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