On 15/12/11, Yun Shi <yunsh...@gmail.com> wrote: > 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.
Yes, see discussion of gen-pairs in manual section 5.7.1 > When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions > excluded from using non-bonded parameters? This is a separate mechanism. Exclusions for non-bonded interactions are applied "on the fly" in mdrun. That doesn't apply to 1-4 parameter generation, but it is necessary for the set of choices of nrexcl, gen-pairs, fudgeXX, [atomtypes], [nonbond_params], [pairtypes] and [pairs] to be consistent. Details vary with the particular force field. Parameters for "bonded" 1-4 interactions (a.k.a. pairs) are generated in grompp according to the rules of the force field - either from the [pairtypes], [pairs] or from scaling depending on the force field and interaction type. Mark > > > > 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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