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.
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= 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>: > 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> > 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 >> >> -- >>> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > ---------------------------------------------------------------- Novo Webmail IFSC -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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