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 >
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