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
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