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
