[gmx-users] another attempt to clarify rlist, rvdw, ...
mic0404 at yahoo.com
Sun Dec 7 19:21:01 CET 2003
The question I am about to ask has been discussed
in this newsgroup before but I did not find
a clear answer and also some of the suggestions
given previously seem to contradict each other,
so once more:
in the gmx manual it says under "Treatment of cutoffs"
"Usually one builds the neighbor list every 10 time
steps or every 20 fs (parameter nstlist). In the
neighbor list all interaction pairs that fall within
rlist are stored. Furthermore, the interactions
between pairs that do not fall within rlist but do
fall within max(rcoulomb,rvdw) are computed during
NS, and the forces and energy are stored separately,
and added to short-range forces at every time step
between successive NS."
in the following paragraph it says:
"Except for the plain cutoff, all of the interaction
functions in Table 4.2 require that neighbor
is done with a larger radius than the rc specified
the functional form, because of the use of charge
groups. The extra radius is typically of the order of
If I understand that correctly this means that
if nstlist>1 the difference between
max(rvdw,rcoulomb) and rlist should alsways be
greater than zero (the manual suggests 0.25 nm)
otherwise one runs the risk of gmx occasionally
not considering interactions between some atoms
that are separated by a distance of less than rlist.
The approprate value for this distance will depend
on the parameter nstlist (and on the system
geometry, temperature, etc).
I wonder if it wouldn't be a good idea for gmx
to check (at best continiously during a simulation)
whether the relation between the parameter nstlist
and the difference between max(rvdw,rcoulomb)
and rlist is reasonable? AFAIK this is not
implemented in gmx, in fact it doesn't even
give a warning if I set nstlist to a high
value and at the same time have
Please let me know your thoughts on this matter
and/or correct me if I am wrong.
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