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 <asara...@if.sc.usp.br>
*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 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 <resa...@yahoo.com <mailto:resa...@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 <apal...@nd.edu <mailto:apal...@nd.edu>>
> To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto: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
<mailto: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
<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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