[gmx-users] nrexcl = 2 or 3?

[Mark Abraham]

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 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111215/f3247441/attachment.html>