On 26/11/2010 3:01 AM, Gavin Melaugh wrote:
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
displayed:
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
charge)
Maybe. Some electrostatics models are sensitive to charge group size for
dealing with cut-offs. PME isn't.
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?
Not really. A charge group is normally chosen to be a heavy atom, plus
perhaps some associated hydrogen atoms, such as a methylene group. Its
radius is smaller than a C-H bond length, so much less than 0.1nm.
Normally the total charge of each charge group should be an integer if
your electrostatics model cares.
Mark
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