[gmx-users] New ion parameters and OPLS-AA
resal81 at yahoo.com
Wed Dec 16 16:42:20 CET 2009
Thank you very much Dr Paluch and Dr van der Spoel for your responses.
Then it seems it would be safer to use mixing the combination rules as a last
resort, although it is comforting to know that other people have used
it before successfully.
I think I will look for the parameters that are compatible with the OPLS-AA combination rule. Although based on Horinek paper I was sort of hoping that I could convert the parameters for different combination rules.
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, December 16, 2009 3:10:13 AM
Subject: Re: [gmx-users] New ion parameters and OPLS-AA
On 12/15/09 11:03 PM, Reza Salari wrote:
> 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.
Unfortunately the combination rules are part of the parameterization,
simply because changing the combination rules means changing the
parameters. Hence I would suggest you look for ion parameters that are
compatible with your force field of choice, alternatively a force field
that is compatible with your ions of choice. Since these ion parameters
were developed by Tom Cheatham I presume that Amber would be a suitable
> 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
> <mailto: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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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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