Hi All,

Recently there has been a new set of ion parameters published by Joung and 
Chetham and I am interested in running some test runs using these parameters. 
These set of parameters are based on using LB rule (arithmetic mean) for sigmas.

However I am using OPLS-AA ff so I am using the combination rule 3 (geometric 
mean of corresponding A and B values). My question is that can I use the exact 
sigma values from Cheatham for my simulations? I'm almost positive that I have 
to change these sigma values to be consistent with the combination rule that I 
am using. In fact there is a paper by Horinek et al that has a nice table of 
different ionic sigma and epsilon values from different parameter sets (Aqvist, 
Jensen, Cheatham,..). The article is here:
http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000130000012124507000001&idtype=cvips&gifs=Yes

In that table, they have mentioned two sigmas; a usual sigma (which is used 
with rule 2) and a sigma prime (which can be used with rule 3). However it 
seems sort of unclear to me how they got these value since in some references 
that they've mentioned I could find either sigma or sigma prime, not both. So I 
am guessing there must be some way to convert these two sigmas to each other.

So does anyone know if there is such way? Does GROMACS internally treats sigmas 
as "sigma prime" for OPLS-AA? I looked at the manual and also searched the 
mailing list to find an explanation but without luck. I really appreciate any 
help on clarifying this.

Regards,
Reza Salari
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