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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.<BR>
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I have found this paper:<BR>
Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of Inaccuracies and Proposed Improvements<BR>
<A href="http://pubs.acs.org/doi/abs/10.1021/jp0765392">http://pubs.acs.org/doi/abs/10.1021/jp0765392</A><BR>
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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.<BR>
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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?<BR>
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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 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 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 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 />¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en la <a href='http://opiniones.msn.es/default.aspx/Futbol/Atletico-de-Madrid ' target='_new'>Zona Fan de MSN Deportes</a></body>
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