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

[Andrew Paluch]

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
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091215/929f9da7/attachment.html>