[gmx-users] nrexcl = 2 or 3?

[lq z]

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." In charmm ff, 1-4 interactions are needed and it is "no further than
3 bonds away," so I should use nrexcl = 2. However, it is 3 in charmm27.ff/
folder.

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.

Your clarification is greatly appreciated.

Luke
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