[gmx-users] x2top and OPLS-AA vs. fudged 1-4 interactions

[Vasilii Artyukhov]

Dear colleagues,

I'm looking for clarifications on what exactly I need to do in order to get
a correct scaling of 1-4 interactions for OPLS-AA in a topology made by
x2top. Specifically, will the command

x2top -f in.gro -o out.top

result in a topology that, when fed into grompp, will give a .tpr that is
correct in this respect? Or should I use the same command with the -nopairs
option and let grompp generate the pairs basing on the [ defaults ] section
of ffoplsaa.itp? Or did I miss the correct way to use x2top altogether
(nexcl=4? something with dihedrals? etc.)?

I'm trying to check if OPLS parameters are suitable for the description of a
somewhat unusual system, and so far, the geometry of the system seems to get
distorted by some intramolecular nonbonded interactions; I'd like to know
whether that's because of unsuitable FF parameters, a bad topology, or both
:)

The version of GROMACS is presently 3.3.3, but I'm actually going to use
4.x. for this once I know how to use x2top properly.

Thanks in advance,
Vasilii
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