Dear All,
I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly ---> gen-pairs = "no" ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 ---> for AMBER99SB only 1 2 no 1.0 0.16666666666666 --- > for both GLYCAM et AMBER99SB ;1 2 yes 1.0 1.0 --> for GLYCAM only #include "ffnonbonded_mod.itp" #include "ffbonded.itp" 2- For the surfactant, I have calculated the pair-types interactions manually with the comb-rule = 2 and divided the values /6 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files 3- For the peptide, I have calculated the pair-types interactions manually comb-rule = 2 and divided the values /10 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files. 4- In the surfactant topology file I have repeated 6 times the [pairs] directives 0.166666*6 ~=10 5 - In the peptide topology file I have repeated 5 times the [pairs] directives 0.166666*5 ~= 0.8333 Is it correct ? However I have a little doubt about "gen-pairs" directive should I have set it to "no" or "yes". in a previous message with a similar problem, the gen directive was set "yes" http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Thank you for your help Stephane
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