ms <[email protected]> schrieb:
On 7/8/14 12:35 PM, Yip Yew Mun wrote: > Hi all, > > I wish to run a MD simulation with the protein in CG and the small organic > ligand in AA. Has anyone attempted this before? If so, can guide me on how to > generate the right topologies for such simulations? > > Thanks, any help would be greatly appreciated. =) > Hi, In our group we run hybrid CG-AA simulations where we *also* leave some of the protein in AA, to ensure a more accurate ligand/protein interaction. You can find a few papers here: http://digitallibrary.sissa.it/bitstream/handle/1963/1745/48_05.pdf?sequence=2 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047332#pone-0047332-g003 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0064675#pone-0064675-g007 In general, generating the topologies etc. for such a simulation very much depends on the specific CG-AA method/setup you are using. I hope it helps, Massimo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
