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

[Yan Chai]

Dear Gromacs users,

    I have a question about the twin range cut-off's in Gromacs.

    If I choose vdwtype as Cut-off, the manual on run parameters tells me
that I need to choose rvdw>=rlist in this case. I have read the section on
the treatment of cutoffs in the manual and also the mailing list. My
understanding on the twin range cut-off's is following:

    1, Every nstlist steps, the neighborlist is updated according to the
cut-off of neighborlist rlist and all interactions are calculated according
to the cut-off of forces, such as rvdw;

    2, Every step, all interactions of atom pairs in the neighborlist are
calculated.

    If my understanding above is correct, it seems that the concept or the
algorithm of neighborlist for the twin range cut-off's in Gromacs is
different from the original concept of Verlet neighborlist which is
discussed in the textbook on MD simulations, for instance, in the book
Understanding Molecular Simulation by Frenkel and Smit. The original
algorithm of Verlet list needs rlist>rvdw in order to contain all particles
which might have interactions. However, the twin range cut-off's in Gromacs
with rvdw>=rlist seems to be contradict to this original idea of Verlet list
and to miss some contribution to the interaction by the particles which stay
between rlist and rvdw in the normal steps without updating the
neighborlist.

    So my question is: what is the idea for Gromacs to take such algorithm
of twin range cut-off's?

    Thanks!

      Yan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090527/0680791b/attachment.html>