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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