From: Juba, Derek (derek.juba_at_nist.gov)
Date: Thu Nov 21 2013 - 11:41:06 CST
Thanks for the tips- I've looked into OpenMM and it seems like it actually may be the best platform for what I'm trying to do.
I do have one more question about NAMD, in case I decide to go that way. The electrostatic calculation I'm doing is producing a global electric field, computed from all atoms. But, as you mentioned, NAMD sometimes expects bonded atoms to be excluded from non-bonded force calculations. If I set the "exclude" parameter to "none", it looks like NAMD will think it should be computing non-bonded interactions between all pairs. Is just doing this sufficient to give correct results for non-bonded interactions being computed between all pairs, or would I also have to modify the parameters for the bonded interactions to account for the fact that the non-bonded forces between even the bonded atoms are being explicitly added in?
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