[gmx-users] Overriding "genpairs=yes" default for one specific molecule? Possible?
wlash at ucalgary.ca
Wed Apr 13 22:50:00 CEST 2005
First, I am sorry if this has come up on the mailing list before - a
quick search didn't reveal anything obvious.
I am in a position where I would like to use a molecular topology in
conjuction with the OPLS-aa protein forcefield, but on first glance they
seem to be incompatible.
My problem is that OPLS uses genpairs=yes and fudgeLJ and fudgeQQ
parameters of 0.5. I would like to override this behavior for this one
specific molecule - e.g. with exclusions. However, after excluding the
automatic calculation of 1-4 non-bonded interactions I need to specify a
set of [pairs] to modify the dihedral functions. Is this possible to do
with the OPLS defaults, or will I have to reparameterize my dihedral
functions for this molecule?
Unfortunately the gromacs manual does not very specifically explain the
precedence of the different topology statements (e.g., do 'exclusions'
override 'pairs' or 'genpairs=yes' directive? Or does genpairs=yes take
precedence over everything?). My initial testing shows that the
topology is unstable if I attempt to first exclude all 1-4 interactions,
then define pairs, with genpairs=yes.
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