On 2/7/13 9:46 AM, Ali Alizadeh wrote:
Dear All user
There are 350 decane molecules in my simulation box,
I like doing a simulation(npt ensemble) by a united atom force field,
Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in
gromacs?
Beside, How can I neglect coloumb interaction(non-bonded) and
dihedrals(bonded)?
The OPLS force field in Gromacs contains both OPLS-AA (all-atom) and OPLS-UA
(united-atom) types, so you could in theory use OPLS-UA, but that's a fairly
ancient force field. In that case, there are no Coulombic interactions anyway,
because the united-atom carbons should not have any charge. If you want to
neglect dihedrals, I think you're hacking the force field in a way that makes no
sense.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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