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Yes, I use PME.<BR> <BR>> Date: Mon, 1 Jun 2009 19:34:27 +0200<BR>> From: spoel@xray.bmc.uu.se<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] crystals of KCl during simulation<BR>> <BR>> Rebeca García Fandiño wrote:<BR>> > Thank you very much for your answer. I have read some recent literature, <BR>> > and you are right, it is a problem about the parameters for ions in Amber.<BR>> > <BR>> > I have found this paper:<BR>> > Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of <BR>> > Inaccuracies and Proposed Improvements<BR>> > http://pubs.acs.org/doi/abs/10.1021/jp0765392<BR>> > <BR>> > There, they simulate nucleic acids using a combination of Amber and <BR>> > OPLS sigma and epsilon for the ions. I have tried that in the case of my <BR>> > protein, just changing the ion sigma and epsilon in the topology by <BR>> > those corresponding to OPLS, but I still observe aggregation for the ions.<BR>> > <BR>> > Would this combination of Amber and OPLS have any kind of potential <BR>> > problem during the simulation? Has anybody any idea to avoid this type <BR>> > of artefact?<BR>> <BR>> Just checking, do you use PME? (You should...)<BR>> > <BR>> > Thank you very much in advance,<BR>> > <BR>> > Rebeca.<BR>> > <BR>> > > To: gmx-users@gromacs.org<BR>> > > Subject: Re: [gmx-users] crystals of KCl during simulation<BR>> > > Date: Mon, 1 Jun 2009 14:34:55 +0200<BR>> > > From: baaden@smplinux.de<BR>> > ><BR>> > ><BR>> > > Hi,<BR>> > ><BR>> > > regafan@hotmail.com said:<BR>> > > >> [..] but after equilibration I have observed that KCl is <BR>> > aggregating, like<BR>> > > >> if it was making crystals. When I used NaCl instead KCl, this not<BR>> > > >> happened.<BR>> > ><BR>> > > >> Does anybody has any idea about the reason of the behaviour of KCl in<BR>> > > >> the simulation?<BR>> > ><BR>> > > This even does happen with Amber :) So my guess is you correctly <BR>> > transferred<BR>> > > the parameters, but stumbled upon an artefact. If you check the recent<BR>> > > literature you may notice that many publications with Amber using K+<BR>> > > only employ minimal (neutralising) salt conditions as a workaround. At<BR>> > > least this is what we did recently [1].<BR>> > ><BR>> > > Marc Baaden<BR>> > ><BR>> > > [1] Interactions between neuronal fusion proteins explored by molecular<BR>> > > dynamics, Biophys.J.94, 2008, 3436-3446.<BR>> > > http://dx.doi.org/10.1529/biophysj.107.123117<BR>> > ><BR>> > > --<BR>> > > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris<BR>> > > mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr<BR>> > > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217<BR>> > ><BR>> > ><BR>> > > _______________________________________________<BR>> > > gmx-users mailing list gmx-users@gromacs.org<BR>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > > Please search the archive at http://www.gromacs.org/search before <BR>> > posting!<BR>> > > Please don't post (un)subscribe requests to the list. Use the<BR>> > > www interface or send it to gmx-users-request@gromacs.org.<BR>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> > <BR>> > ------------------------------------------------------------------------<BR>> > ¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en la Zona <BR>> > Fan de MSN Deportes <BR>> > <http://opiniones.msn.es/default.aspx/Futbol/Atletico-de-Madrid ><BR>> > <BR>> > <BR>> > ------------------------------------------------------------------------<BR>> > <BR>> > _______________________________________________<BR>> > gmx-users mailing list gmx-users@gromacs.org<BR>> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > Please search the archive at http://www.gromacs.org/search before posting!<BR>> > Please don't post (un)subscribe requests to the list. Use the <BR>> > www interface or send it to gmx-users-request@gromacs.org.<BR>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> <BR>> <BR>> -- <BR>> David.<BR>> ________________________________________________________________________<BR>> David van der Spoel, PhD, Professor of Biology<BR>> Dept. of Cell and Molecular Biology, Uppsala University.<BR>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>> phone: 46 18 471 4205 fax: 46 18 511 755<BR>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<BR>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><br /><hr />Más rápido, fácil, seguro y con lo que más te gusta de Windows Live, así es el nuevo Internet Explorer 8 <a href='http://ie8.msn.com/microsoft/internet-explorer-8/es-es/ie8.aspx' target='_new'>¡Descárgatelo! </a></body>
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