[gmx-users] Question about cut-off values with respect to the neighbor list

Andrew DeYoung adeyoung at andrew.cmu.edu
Sat Aug 18 23:59:26 CEST 2012


If you have time, I have some questions about the neighbor list and cut-off

I am running NVT simulations with coulombtype = PME and vdwtype = cut-off.
I have specified equal neighbor search, vdw, and Coulomb cut-offs: rlist =
1.5 nm, rvdw = 1.5 nm, rcoulomb = 1.5 nm.  Is it a good idea to use rlist =
rvdw = rcoulomb?  (I typically use the default value of nstlist: nstlist =

According to the manual
(http://manual.gromacs.org/current/online/mdp_opt.html#vdw), using vdwtype =
cut-off means that neighbor searching will be performed using a twin-range
approach.  rvdw must be greater than or equal to rlist, rvdw >= rlist; in my
case, I am using rvdw = rlist.  Is this a good idea?

Section 4.6.3 of the manual describes.  Of course, in the neighbor list,
"all interaction pairs within rlist are stored."  But "interactions between
pairs that do not fall within rlist but do fall within max(rcoulomb,rvdw)
are computed during neighbor searching."  Does this statement imply that I
should use rvdw > rlist, rather than rvdw = rlist?

However, there is no "grace distance" in Gromacs
According to Berk Hess:

"There is no 'grace distance' in Gromacs. A pair of atoms is put in the
neighborlist if the centers of geometry of the charge groups they belong to
are inside the cut-off distance. Thus some atom pairs might not interact
while they are inside the cut-off distance, while other atom pairs might
interact while they are outside the cut-off distance. These charge groups
are important for simulations with cut-off electrostatics as they reduce the
cut-off noise significantly. With shiftted electrostatics or PME charge
groups are only important for performance reasons."

The above paragraph seems to imply that I should use rvdw = rlist.  The
above paragraph seems to say that since, unlike other MD codes that do not
use charge groups, in Gromacs there is really no need for a "grace distance"
-- because the use of charge groups, rather than atoms, in a sense has a
"bult-in" grace distance.  The charge groups are unlikely to move much
between neighbor list updates every nstlist steps.

So, my question is, am I at risk for artifacts if I use rvdw = rlist?
Should I instead use rvdw >= rlist?  

(I am using nstlist = 10 with a liquid that I anneal from 700 K down to 350

Thank you kindly!

Andrew DeYoung
Carnegie Mellon University

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