[gmx-users] Doubts in combination rules 2 and 3
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jun 11 15:10:19 CEST 2018
Den 2018-06-11 kl. 11:20, skrev Apramita Chand:
> Please clarify these following doubts regarding combination rules in gromos
> force field:
> 1. The ffnonbonded.itp contains c6, c12 terms. If I choose combination rule
> 1 , it takes V and W as C6 and C12 as given. If combination 2 or 3 are
> chosen , then are the values converted to sigma and epsilon (Since for
> V=sigma and W=epsilon) and then used?
The other way around. If you have combination 2 or 3 the numbers are
interpreted as sigma and epsilon and converted to C6 and C12 by grompp.
Use gmx dump -s topol.tpr to check.
> 2. If I have sigma and epsilon values for my molecule of interest, how do I
> add them to ffnonbonded.itp? Can I directly include sigma value under C6
> and epsilon value under C12 column?
> And then specify combination rule as 2 or 3?
> If so, how should I modify the non-bonded params section?
> Should I compute the interactions between atoms(according to the
> combination rule) and include them prior to simulation??
> Thanking you,
> Yours sincerely,
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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