[gmx-users] Doubts in combination rules 2 and 3
apramita.chand at gmail.com
Mon Jun 11 11:20:51 CEST 2018
Please clarify these following doubts regarding combination rules in gromos
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?
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??
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