[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.

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

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

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, 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