[gmx-users] nrexcl = 2 or 3?

[Yun Shi]

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.abraham at anu.edu.au>wrote:

>
>
> On 15/12/11, *lq z *<lqz.fsu at 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
>
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