[gmx-users] New ion parameters and OPLS-AA
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
Wed Dec 16 17:36:50 CET 2009
If you decide to change the ions parameters, you can use the method
It is relatively fast and provide nice parameters.
Alexandre Suman de Araujo
Instituto de Física de São Carlos
Universidade de São Paulo
São Carlos - Brasil
Citando Reza Salari <resal81 at yahoo.com>:
> Thanks for your response.
> While I will try that (although it seems it needs quite amount of
> scripting), I remember in the past some people in the mailing list
> mentioned problems while using nonbond_params directvie with OPLS-AA
> and in response it was generally suggested to avoid doing this kind
> of mixing. Like Dr Abraham suggestion here:
> Have you tried this kind of mixing for OPLS successfully, without
> being overridden by the default rules?
> The main thing that I am still unsure about is how the previously
> mentioned paper converted the sigma values for different combination
> rules. It seems that there must be a relatively direct way to do
> this without going through the re-parametrization process.
> Reza Salari
> From: Andrew Paluch <apaluch at nd.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tue, December 15, 2009 4:34:18 PM
> Subject: Re: [gmx-users] New ion parameters and OPLS-AA
> 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
>> 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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