Thank you very much, André. Could you please indicate me how could I use these parameters in Gromacs? I have not seen them included in ions.itp and I could not find anything in the manual.
Best wishes, Rebeca. > Date: Mon, 1 Jun 2009 14:52:35 -0300 > Subject: RE: [gmx-users] crystals of KCl during simulation > From: [email protected] > To: [email protected] > > Hi Rebeca, > > I found out a few years ago that OPLS parameters for Na+ were inadequate > for my simulations on surfactants aggregation due to the formation of > stable (and unrealistic) ionic bridges. I got better structures using > Aqvist's parameters (available in GROMACS), maybe you could try these > parameters for K+ as well. > > please let me know if that works. > > best regards, > > André > > > > > > Yes, I use PME. > > > >> Date: Mon, 1 Jun 2009 19:34:27 +0200 > >> From: [email protected] > >> To: [email protected] > >> Subject: Re: [gmx-users] crystals of KCl during simulation > >> > >> Rebeca García Fandiño wrote: > >> > Thank you very much for your answer. I have read some recent > >> literature, > >> > and you are right, it is a problem about the parameters for ions in > >> Amber. > >> > > >> > I have found this paper: > >> > Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of > >> > Inaccuracies and Proposed Improvements > >> > http://pubs.acs.org/doi/abs/10.1021/jp0765392 > >> > > >> > There, they simulate nucleic acids using a combination of Amber and > >> > OPLS sigma and epsilon for the ions. I have tried that in the case of > >> my > >> > protein, just changing the ion sigma and epsilon in the topology by > >> > those corresponding to OPLS, but I still observe aggregation for the > >> ions. > >> > > >> > Would this combination of Amber and OPLS have any kind of potential > >> > problem during the simulation? Has anybody any idea to avoid this type > >> > of artefact? > >> > >> Just checking, do you use PME? (You should...) > >> > > >> > Thank you very much in advance, > >> > > >> > Rebeca. > >> > > >> > > To: [email protected] > >> > > Subject: Re: [gmx-users] crystals of KCl during simulation > >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200 > >> > > From: [email protected] > >> > > > >> > > > >> > > Hi, > >> > > > >> > > [email protected] said: > >> > > >> [..] but after equilibration I have observed that KCl is > >> > aggregating, like > >> > > >> if it was making crystals. When I used NaCl instead KCl, this not > >> > > >> happened. > >> > > > >> > > >> Does anybody has any idea about the reason of the behaviour of > >> KCl in > >> > > >> the simulation? > >> > > > >> > > This even does happen with Amber :) So my guess is you correctly > >> > transferred > >> > > the parameters, but stumbled upon an artefact. If you check the > >> recent > >> > > literature you may notice that many publications with Amber using K+ > >> > > only employ minimal (neutralising) salt conditions as a workaround. > >> At > >> > > least this is what we did recently [1]. > >> > > > >> > > Marc Baaden > >> > > > >> > > [1] Interactions between neuronal fusion proteins explored by > >> molecular > >> > > dynamics, Biophys.J.94, 2008, 3436-3446. > >> > > http://dx.doi.org/10.1529/biophysj.107.123117 > >> > > > >> > > -- > >> > > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > >> > > mailto:[email protected] - http://www.baaden.ibpc.fr > >> > > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 > >> > > > >> > > > >> > > _______________________________________________ > >> > > gmx-users mailing list [email protected] > >> > > http://www.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 [email protected]. > >> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > >> > ------------------------------------------------------------------------ > >> > ¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en la > >> Zona > >> > Fan de MSN Deportes > >> > <http://opiniones.msn.es/default.aspx/Futbol/Atletico-de-Madrid > > >> > > >> > > >> > ------------------------------------------------------------------------ > >> > > >> > _______________________________________________ > >> > gmx-users mailing list [email protected] > >> > http://www.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 [email protected]. > >> > 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 > >> [email protected] [email protected] http://folding.bmc.uu.se > >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> http://www.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 [email protected]. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _________________________________________________________________ > > Recibe toda las noticias de actualidad al instante en tu Messenger > > http://especiales.es.msn.com/noticias/msninforma.aspx > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.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 [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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. 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