Thank you very much Dr Paluch and Dr van der Spoel for your responses. Then it seems it would be safer to use mixing the combination rules as a last resort, although it is comforting to know that other people have used it before successfully.
I think I will look for the parameters that are compatible with the OPLS-AA combination rule. Although based on Horinek paper I was sort of hoping that I could convert the parameters for different combination rules. Regards, Reza Salari ________________________________ From: David van der Spoel <sp...@xray.bmc.uu.se> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wed, 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 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. Unfortunately the combination rules are part of the parameterization, simply because changing the combination rules means changing the parameters. Hence I would suggest you look for ion parameters that are compatible with your force field of choice, alternatively a force field that is compatible with your ions of choice. Since these ion parameters were developed by Tom Cheatham I presume that Amber would be a suitable force field. > > 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 > <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 > > -- > gmx-users mailing list gmx-users@gromacs.org > <mailto: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 > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- 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
-- 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
