Hello,
I compared the LJ parameters for the interaction Potassium - backbone carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the forcefield. I found different numbers for the sigma value i cannot explain to myself: The stock charmm36 implementation has the following LJ parameters for potassium and oxygen: ; atom Emin (kcal/mol) Rmin/2 (A) POT 0.087 1.76375 O 0.120 1.7 Converting the above values to units used in gromacs (kJ/mol and nm) and applying standard combination rules this should give the following nonbonded energy parameters: [ pairtypes] ; sig = (Rmin,i/2 + Rmin,j/2)/10 ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ ; i j func sig (nm) eps (kj/mol) O POT 1 0.346 0.4275 However, the actual entry for the interaction in GROMACS/charmm36 has the energy minimum at a much smaller distance (epsilon is on the point though!) ; i j func sig (nm) eps (kJ/mol) O POT 1 0.282 0.4275 Can somebody tell me the reason for this huge difference? Is there an error in my calculation? I am trying to convert an NBFIX applied to this specific interaction to gromacs. However, I am not sure how to proceed without doing the reparametrization in gromacs again, because the stock values differ that much. Best regards, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt [email protected] Don't trust atoms, they make up everything. -- 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 [email protected].
