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: sp...@xray.bmc.uu.se >> To: gmx-users@gromacs.org >> 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: gmx-users@gromacs.org >> > > Subject: Re: [gmx-users] crystals of KCl during simulation >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200 >> > > From: baa...@smplinux.de >> > > >> > > >> > > Hi, >> > > >> > > rega...@hotmail.com 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:baa...@smplinux.de - http://www.baaden.ibpc.fr >> > > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 >> > > >> > > >> > > _______________________________________________ >> > > gmx-users mailing list gmx-users@gromacs.org >> > > 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 gmx-users-requ...@gromacs.org. >> > > 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 gmx-users@gromacs.org >> > 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 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://folding.bmc.uu.se >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> 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 gmx-users@gromacs.org > 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 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://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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