[gmx-users] another attempt to clarify rlist, rvdw, ...

m b mic0404 at yahoo.com
Sun Dec 7 19:21:01 CET 2003

dear gmx-users,

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

 0.25 nm"

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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