[gmx-users] charge group radii
gmelaugh01 at qub.ac.uk
Mon Nov 29 16:25:01 CET 2010
Cheers Mark for the reply
I was more concerned about the Van der Waals interactions. If the
distance between the centre of geometry of two charge groups is larger
than rlist then these interactions are not included. I was therefore
concerned if I had a situation in which certain atoms of a charge group
(6 atoms) where close enough to interact with atoms of another charge
group, but the COGs of the charge groups were larger than rlist, then
these interactions would not be accounted for. Is this true?
Mark Abraham wrote:
> 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
>> NOTE 3 [file pbc.mdp]:
>> The sum of the two largest charge group radii (0.602793) is larger
>> 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
> 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.
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