[gmx-users] New ion parameters and OPLS-AA
resal81 at yahoo.com
Wed Dec 16 18:56:23 CET 2009
Thank you very much. That sounds interesting!
BTW, I finally found out that the only way to use parameters developed using different combination rules together, is to define them manually in nonbonding_params section of topology. This sounds a little bit dangerous since it is sort of mixing different approaches.
From: Alexandre Suman de Araujo <asaraujo at if.sc.usp.br>
To: gmx-users at gromacs.org
Sent: Wed, December 16, 2009 11:36:50 AM
Subject: Re: [gmx-users] New ion parameters and OPLS-AA
If you decide to change the ions parameters, you can use the method described here:
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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