Re: [gmx-users] nrexcl = 2 or 3?

On 15/12/11, Yun Shi 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 s

Re: [gmx-users] nrexcl = 2 or 3?

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

Re: [gmx-users] nrexcl = 2 or 3?

On 15/12/11, lq z 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),

[gmx-users] nrexcl = 2 or 3?

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? 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."