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
