[gmx-users] The meaning of rlist and rcoulomb for coulombtype=reaction-field
John D. Chodera
jchodera at gmail.com
Wed Jan 10 01:02:19 CET 2007
I am having a difficult time understanding the meaning of 'rlist' and
'rcoulomb' when the reaction-field treatment of electrostatics is used.
After explaining the twin-range cutoff method (which seems to be
fairly straightforward) which explains the case where rlist <
rcoulomb, the manual states:
"Except for the plain cutoff, all of the interaction functions in
Table 4.2 require that neighbor searching is done with a larger
radius than the r_c specified for the functional form, because of the
use of charge groups. The extra radius is typically of the order of
This appears to suggest that for reaction-field, we would wish to set
rlist = rcoulomb + 0.25 nm, something which grompp does not allow.
From my experience with molecular simulation, it seems to be
desirable to ensure that the neighbor list maintained between the
times neighbor searching is conducted is indeed larger than the
cutoff beyond which electrostatic interactions are zero.
Does this 0.25 nm buffer get automagically added to the specified
rcoulomb to determine the neighbor searching radius? Also, what
happens when rlist < rcoulomb for reaction-field? Is the standard
twin-range method employed here? Finally, I have very little
experience with reaction-field -- is there a recommended combination
for rlist and rcoulomb for simulations of small protein systems?
Apologies if this topic has been addressed before, but I was not able
to clear up my foggy understanding from searching through the mailing
John Chodera <jchodera at ugcs.caltech.edu> | Mobile : 415 867-7384
Graduate Group in Biophysics, Dill lab | Lab phone : 415 514-4290
University of California, San Francisco | Lab fax : 415 502-4222
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