[gmx-users] The meaning of rlist, rvdm and rcolumn

Li Dawei phyldw at nus.edu.sg
Tue Jul 27 05:42:40 CEST 2004

Dear all:

I searched this mailing list but become even more confused. Who can help
to clarify the exact meaning of these parameters. 

I copied this from this list, which said what I want and seemed got no


Li, Dawei

dear all,

I do MD simulations using a cutoff for
both VdW and Coulomb interactions.
I am rather confused about the
parameters used in the input file.
(rlist, rvdw, rcoulomb)
I searched this mailing list
for clarification, but I found two
statements that appear to contradict
each other (just as the documentation
does by the way). The two mails are: 

Normally I would assume that if one uses
a neighbour list there are (at least) two cutoffs:
One for a sphere around each atom with ALL
(and only) the atoms in this sphere considered when
calculating the energy and the forces on
the primary atom at EACH time step (rvdw,
rcoulomb ?).
A second (larger) cutoff that is used when
calculating the neighbour-list at intervals
of each 10 (or so) time steps (rlist ?)
were of course rlist > rvdw and rcoulomb.
(it is also possible to have the program
calculate this parameter nstlist automatically
thereby optimizing the performance, this is
not implemented in Gromacs, is it ?)
If one uses a switched potential there
is a third cutoff (the onset of the switching
function) that would be shorter than
rvdw and rcoulomb.

this implies: rlist > rvdw,rcoulomb > r*_switch
... in contrast to (part of) the docu, and the
errormsg given by the code, and to one of the
messages cited above.(the message of Anton
Feenstra reminds me rather of another concept,
namely the multiple timestep algoritm which, if 
I am not mistaken, is not implemented
in Gromacs)
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