[gmx-users] Energy groups

[Gavin Melaugh]

Hi all

If I have a topology with set up below (excerpts). And define energy
groups in the .mdp file say 'virtsites' and 'endgroup' in correspondence
with the index file.  Will defining energygrp_exl 'virtsites' and
'endgroup' prevent nonbonding interactions between any atom in either of
these groups. Also will all other nonbonding interactions stated in the
topology remain the same?

Many Thanks

Gavin

;Parameter level
[defaults]
; nbfunc    comb-rule     gen-pairs        fudgeLJ     fudgeQQ
     1         3              yes            0.5         0.5

[atomtypes]
;type     mass           charge      ptype     sigma(nm)   
epsilon(kjmol-1)
   CB     12.011000      0.000000       A      0.355000      0.292880
   CA     12.011000     -0.115000       A      0.355000      0.292880
   HC      1.008000      0.115000       A      0.242000      0.125520
   CU     13.019000      0.265000       A      0.350000      0.334720
   NU     14.007000     -0.597000       A      0.325000      0.711280
   CH     13.019000      0.332000       A      0.385000      0.334720
   C3     15.035000      0.000000       A      0.391000      0.669440
   C2     14.027000      0.000000       A      0.390500      0.493712
   VS      0.0           0.0            V      0.0           0.0

[nonbond_params]
;i  j  funct  sigma  epsilon
VS  C3  1      0.1    0.03153