On 30/11/2010 2:25 AM, Gavin Melaugh wrote:
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?
Something along those lines is true - I forget the details. Charge
groups moving in and out of neighbour lists is a source of algorithmic
noise that affects non-PME models. Making them small in radius, small in
numbers of atoms, of integral charge, and with larger neighbour-list
radius reduces these effects. However the VDW interaction strength has
decayed to zero faster than the Coulomb, so the latter is a more
important effect.
Mark
Gavin
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
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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