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Dear GMX-users. I'm trying to do free energy calculations for calculations of partitions coefficients. My normal defaults section of TraPPE topologies are: ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 no 0.5 0.5 because TraPPE don't use 1-4 LJ interaction, and I have read that FudgeQQ always apply even though gen-pairs=no. Now I want to do my calculations with OPLS-AA for the solute molecule, and TraPPE-UA for the solvent, so my default section must now be: ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.5 , but the problem arises when I have for instance Ethanol in my solvent, then gen-pair will calculate LJ 1-4 interactions for the Ethanol as well. But if I in the .top for the ethanol pair write: [ pairs ] ; ai aj funct c6 c12 1 4 1 0.000000e+00 0.000000e+00; then will the 1-4 LJ be 0, but the 1-4 Coulomb will still be calculated - right?? Also, can I check all the interaction parameters calculated and inserted by grompp? Best regards. Rasmus Lundsgaard |
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