[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  
0.25 nm"

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  
list archives.


- John

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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