[gmx-developers] couple_moltype adds exclusions. why?

David van der Spoel spoel at xray.bmc.uu.se
Sun Nov 25 21:46:15 CET 2012


I'm trying to desolvate a toluene molecule in order to compute the free 
energy of solvation. Using mdp settings

free_energy              = yes
couple-moltype           = toluene

all the non-bonded interactions within the molecule are excluded. Why? 
The 1-4 interactions are not taken away, which should lead to imbalance 
in the intramolecular interactions. Or am I missing something?

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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