Hi: I am looking for indications how to insert a large trimer CG protein into one of the pre-equilibrated bilayers (preferably POPC, if it exists) of the MARTINI web site. And surround the whole with a layer of water, if possible. I have already prepared the .itp file for the trimer, that is, if I did correctly, the CG knows the secondary structure of the trimer..
New to both GROMACS and MARTINI, I have experience how to that job all-atoms with AMBER. There, a cavity into the hydrated bilayer is first created, shaped on the protein to host. For the moment I am at GROMACS 3.3 on a parallel machine. Thanks for help francesco pietra _______________________________________________ gmx-users mailing list [email protected] http://lists.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
