[gmx-users] charge group radii

[Mark Abraham]

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