[gmx-users] Twin range cut-off's: rlist and rvdw

Yan Chai chai.yan.em at googlemail.com
Wed May 27 14:33:19 CEST 2009

On Wed, May 27, 2009 at 1:36 PM, Jussi Lehtola <jussi.lehtola at helsinki.fi>wrote:

> In the twin range method [1] interactions that are in the range
> rlist..rvdw are only calculated during neighborlist updates. In the mean
> time they are considered to stay constant.
> The idea behind this is that when r>rlist the interactions are weaker
> and also vary more slowly, thus one doesn't need to be as precise in
> taking those interactions into account.
> [1] http://dx.doi.org/10.1002/prot.340060203

Thanks for your explanation and the link for the reference.

I think you are right. The interactions between pairs within the range
rlist..rvdw are computed and stored when neighborlists are updated,  and
added  as constant to short-range forces within rlist at every step between
successive neighborlist updates.

It seems that in the twin range cut-off method, rlist does not only play a
role as a cut-off for neighbor searching, but also as a cut-off for
short-range interactions. Do I understand correctly?

I also agree with you that interactions are weak when r>rlist. So it seems
reasonable to use this twin range cut-off algorithm.

However, if we compare the original Verlet list algorithm and the twin range
cut-off algorithm, I think there is a shorting coming of the twin range
cut-off algorithm to consider the particles which diffuse and across the
boundary of rlist between successive neighborlist updates. The particles
which move into the radius of rlist will not be calculated between
successive neighborlist updates. On the other hand, some particles can move
out of the radius of rlist between successive neighborlist updates. If rlist
is really a cut-off for short range interaction, such out moving particle
will not bring too much trouble for the calculation of forces. However, if
rlist is only a cut-off for neighbor searching but not for short range
interactions, such out moving particles will give a particle-based cut-off
for short range interaction rather than a well-defined distance-based
cut-off for forces.

Do people think the effect of these inward moving and outward moving
particles is small and  the  error  for  calculation can be tolerated?


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090527/6fd8ac89/attachment.html>

More information about the gromacs.org_gmx-users mailing list