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

eladp at post.tau.ac.il eladp at post.tau.ac.il
Wed Dec 16 08:11:23 CET 2009

Hi Reza,

> ------------------------------
> Message: 4
> Date: Tue, 15 Dec 2009 14:03:36 -0800 (PST)
> From: Reza Salari <resal81 at yahoo.com>
> Subject: Re: [gmx-users] New ion parameters and OPLS-AA
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <858209.12986.qm at web35303.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
> 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?

I have successfully done so.
My topology looks like this:

#include "ffoplsaa.itp"

[ nonbond_params ]
     opls_272       opls_412  1 0.277  1.2857

#include "frm.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"


Of course there should be a line for every possible pair interaction.
It is important to put the [ nonbond_params ] after the include to  

> 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>
> 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,
> Andrew
> 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
>> here:
>> 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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