On 15/12/11, lq z <lqz....@gmail.com> wrote: > Dear GMXers, > > I need to use charmm ff (same question for amber ffs), and am confused with > what value I should give to nrexcl in [ moleculetype ], 2 or 3?
Whatever value pdb2gmx generates for CHARMM, probably 3. > > > According to the manual (v 4.5), "nrexcl = 3 stands for excluding non-bonded > interactions between atoms that are no further than 3 bonds away." In charmm > ff, 1-4 interactions are needed and it is "no further than 3 bonds away," ... but 1-4 interactions are regarded as bonded interactions. > so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. Yes, CHARMM has special parameters for some 1-4 interactions, which are dealt with seperately. > > > > By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have > charges. If I use nrexcl =3, no electrostatics energy is reported while the > value matches with the one calculated by hand when I set nrexcl to be 2. > As expected. Mark
-- 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
