But the problem is: how to define a boundary? 2008/10/10 Xavier Periole <[EMAIL PROTECTED]>
> 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 > -- Sun Li Department of Physics Nanjing University, China
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