Hi Mark, I do not quite understand. For example, in amber ff, 1-4 interactions (except the part from dihedral interactions) are calculated according to non-bonded parameters and then scaled by 1/2 or 5/6. When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions excluded from using non-bonded parameters?
Thanks, Yun On Wed, Dec 14, 2011 at 4:33 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > > > 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 >
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