[gmx-users] New ion parameters and OPLS-AA
apaluch at nd.edu
Tue Dec 15 22:34:18 CET 2009
Read the manual. You can explicitly declare all of your cross terms rather
than using the same mixing rule for all terms. You can easily write a
script to modify your input files accordingly,
On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari <resal81 at yahoo.com> wrote:
> 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:
> 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.
> Reza Salari
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