Hi, As mentioned by others, there's really lots of literature out there. I thought I mention a recent study we carried out, because it actually helped discover some new ion binding sites based on MD. By re-examining crystal structures based on these results, we could even find experimental evidence for those ions being there. [1]
But actually you didn't tell us which ions you want to simulate? Monovalent ions should be sort of ok, although there are differences among the forcefields (some original KCl used to crystallize). Di-valent ions, in particular Ca2+, are much more tricky. Higher charged ones are a nightmare. The higher the charge, the more likely you might want things like polarization in your simulation. There are also some specific forcefields finely parameterized for ions based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh and Piquemal. Good luck, Marc [1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000 [2] SIBFA (Sum of Interactions Between Fragments Ab initio computed) http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html [email protected] said: >> Thankx for the reply ... >> Can you refer some papers which can be helpful for me to do MD >> simulation of proteins with ions ... It will be of great help.. I >> searched the gromacs user list but couldn't get much material.. -- 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
