Hi Chris, Sorry to repost the same question, but I have really tested your method the last few weeks. My question about the gen-pairs directive come from the fact that I have read a message from you
http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Where you detailed how to use the Berger and OPLS force fields together in the same system. By reading carefully the meaning of the gen-pairs directive, I found several errors in my force field. BYW in your previous message http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html In the step 3, I think there is a typo, it is "values/10" instead of "values/12". Am I right? Thank you again Stephane Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the manual and reading about pairs, gen-pairs, and pairtypes. I think that this is one case where you would benefit more from fully understanding how these parts work than from a direct answer to your question. If you are having problems, please provide a whole bunch more information on the problems that you are seeing. If, on the other hand, you are just looking for somebody other than me to comment on the accuracy of the April post, then that is perfectly fine with me, but you should state that. Chris. -- original message -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
