Hey all, I have been reading many post about this issue, but still do not have a clear answer.
I am using the AMBER force-field where 1-4 interactions are scaled (fudgeLJ = 0.5 and fudgeQQ = 0.8333). In addition I use parameters of molecules that require the 1-4 interaction to NOT be scaled. What I did to solve this issue is the follwoing: In the molecules *itp file I listed all 1-4 interactions explicitly. I used the pairs type 2, as in here: [ pairs ] 1 14 2 1 0.161 0.175 0.339967 0.457730 As you can see, I use fudgeQQ=1, with the "Real" charges, and the needed LJ parameters. I think this works properly, and that it is equivalent (for the molecule of interest) to use "type 1" with no explicit parameters (that will be accordingly generated from ffnonbonded.itp), along with a forcefield.itp that sets the fudge factors to 1.0. What worries me is that the manual says "type 2" is used for free energy simulations and TI. Can I still use it as mentioned above? Am I missing something? Thanks much, Liel -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.