Thanks for your response. So basically since the Cheatham parameters are using LB rule, I can never use them with OPLS-AA?
I was thinking if I find the parameters for OPLS atoms that are based on geometric rule (if there such a thing exists at all), I could use them along with Cheatham parameters and then define the hetero-atomic LJ parameters in nonbonding_params section. This way I would be mixing parameters that have been developed the same way (regarding combination rules). I understand that one shouldn't directly mix the sigma's that have been developed using different combination rules. If I there is no OPLS parameters based on LB rule, as you mentioned I have to switch to some ff like Amber. 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 1:08:58 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA > > 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. NO don't do that! You will not be using the same parameters, if you change the combination rules. > > 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 > > <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 <mailto: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 <mailto:apal...@nd.edu>> > > To: Discussion list for GROMACS users <gmx-users@gromacs.org > > <mailto: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 > >> > > > > > ---------------------------------------------------------------- > Novo Webmail IFSC > > -- > 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. ________________________________________________________________________ David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- 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