Hi Reza,
------------------------------
Message: 4
Date: Tue, 15 Dec 2009 14:03:36 -0800 (PST)
From: Reza Salari <resa...@yahoo.com>
Subject: Re: [gmx-users] New ion parameters and OPLS-AA
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <858209.12986...@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 <apal...@nd.edu>
To: Discussion list for GROMACS users <gmx-users@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 <resa...@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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