On Fri, 10 Oct 2008 15:09:31 +0800 "Lee Soin" <[EMAIL PROTECTED]> wrote:
Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this? Will the removal of the periodic boundary condition be OK?
The removal of the periodic boundary conditions will be equivalent to an infinite box. Unless you define the boundaries of your box (e.g. walls) the protein (in solvent?) would not stop diffusing. This no problem but is this what you like?
-- Sun Li Department of Physics Nanjing University, China
----------------------------------------------------- XAvier Periole - PhD - Molecular Dynamics Group - NMR and Computation University of Groningen The Netherlands ----------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
