[gmx-users] New ion parameters and OPLS-AA

[Reza Salari]

Thanks for your response.

So basically since the Cheatham parameters are using LB rule, I can never use them with OPLS-AA?

I was thinking if I find the parameters for OPLS atoms that are based on geometric rule (if there such a thing exists at all), I could use them along with Cheatham parameters and then define the hetero-atomic LJ parameters in nonbonding_params section. This way I would be mixing parameters that have been developed the same way (regarding combination rules).

I understand that one shouldn't directly mix the sigma's that have been developed using different combination rules. If I there is no OPLS parameters based on LB rule, as you mentioned I have to switch to some ff like Amber.

Regards,
Reza Salari




________________________________
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 1:08:58 PM
Subject: Re: [gmx-users] New ion parameters and OPLS-AA

> 
> 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.

NO don't do that! You will not be using the same parameters, if you change the combination rules.

> 
> Regards,
> Reza Salari
> 
> ------------------------------------------------------------------------
> *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:
> 
> http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255D&searchHistoryKey <http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255D&searchHistoryKey>=
> 
> It is relatively fast and provide nice parameters.
> 
> Cheers
> 
> --Alexandre Suman de Araujo
> Instituto de Física de São Carlos
> Universidade de São Paulo
> São Carlos - Brasil
> 
> 
> Citando Reza Salari <resal81 at yahoo.com <mailto: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:
> >
> > http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html
> >
> > 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.
> >
> > Regards,
> > Reza Salari
> >
> >
> >
> > ________________________________
> > From: Andrew Paluch <apaluch at nd.edu <mailto:apaluch at nd.edu>>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org <mailto: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,
> >
> > Andrew
> >
> >
> > 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:
> >> http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000130000012124507000001&idtype=cvips&gifs=Yes <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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> 
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-- David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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