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

[David van der Spoel]

>
> 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.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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