Hi all, I'm trying to simulate a protein with the CHARMM36 forcefield. I'm using PME for VdW interactions and since the CHARMM forcefield uses Lorentz-Berthelot combining rules I set *lj-pme-comb-rule = Lorentz-Berthelot *in my mdp file. When I try run grompp with the following command
gmx grompp -f npt_umbrella.mdp -c ang5.gro -p ../topol.top -n ../groups.ndx -o npt5.tpr -po nptOut.mdp I get the following warning "WARNING 1 [file npt_umbrella.mdp]: You are using arithmetic-geometric combination rules in LJ-PME, but your non-bonded C6 parameters do not follow these rules." So I checked my topol.top file to ensure that I was using the correct forcefield and indeed topol.top contains *#include "./charmm36.ff/forcefield.itp". *Looking at forcefield.itp the [ default ] section is as follows. ; This GROMACS version was created from: ; CHARMM parameters: multiple files ; CHARMM topology: multiple files ; Please see forcefield.doc for files and references [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 >From sections 4.1.1 and 5.3.2 in the reference manual, comb-rule 2 corresponds to Lorentz-Berthelot rules. So I'm a bit confused by why the warning is generated. I did also try with *lj-pme-comb-rule *set to *Geometric*, but this again generated a note, instead of a warning this time, that my non-bonded C6 parameters do not follow these rules. Clearly, I'm missing something and I'd appreciate if someone could help me figure out these warnings/notes. I should also mention that I'm using Gromacs-2016-beta2 version (the latest available on the cluster that I use) but I've also tried it on gromacs-2016.4 on my local machine and got the same warnings. Regards, Shrinath -- 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.
