ubject: 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 sect
* 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&searchHistoryK
different approaches.
Regards,
Reza Salari
From: Alexandre Suman de Araujo
To: gmx-users@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
ards,
Reza Salari
From: Andrew Paluch
To: Discussion list for GROMACS users
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
, December 16, 2009 3:10:13 AM
Subject: Re: [gmx-users] New ion parameters and OPLS-AA
On 12/15/09 11:03 PM, Reza Salari wrote:
> 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
Cheatham I presume that Amber would be a suitable
force field.
Regards,
Reza Salari
*From:* Andrew Paluch
*To:* Discussion list for GROMACS users
*Sent:* Tue, December 15, 2009 4:34:18 PM
*Subject:* Re: [gmx-users] New ion
Hi Reza,
--
Message: 4
Date: Tue, 15 Dec 2009 14:03:36 -0800 (PST)
From: Reza Salari
Subject: Re: [gmx-users] New ion parameters and OPLS-AA
To: Discussion list for GROMACS users
Message-ID: <858209.12986...@web35303.mail.mud.yahoo.com>
Content-Type: text
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
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 wrote:
> Hi All,
>
> Recently there has been a ne
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 combi
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