[gmx-users] charge group radii

Gavin Melaugh gmelaugh01 at qub.ac.uk
Thu Nov 25 17:01:34 CET 2010

Hi all,

I have recently been testing out the new version of Gromacs. To do so I
have used files from previous simulations in Gromacs-4.0.7. When feeding
the three files (mdp,gro, and top) into grompp, the following note is

NOTE 3 [file pbc.mdp]:
  The sum of the two largest charge group radii (0.602793) is larger than
  rlist (1.500000) - rvdw (1.400000)

This note did not occur in the previous version and it has led to me to
ask some questions.

1)  I had previously hydrocarbon chains (6-7 carbons long) assigned to
individual charge groups, and never any note. Does this mean that my
previous simulations have artefacts? (all charge groups have zero net
2) If I am happy with the values of rlist and rvdw, will it not be
pretty difficult to assign a charge group with radius < 0.1nm?

Many Thanks


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