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