I'm going to put two peptide chains in a box and study dimerization. I think confining them in a box can reduce conformational search.
2008/10/14 Jochen Hub <[EMAIL PROTECTED]> > Lee Soin wrote: > > Hello, all! I intend to simulate a protein confined in a box. Can anybody > > tell me how to define a boundary, or a wall, in GROMACS? Thanks! > > As far as I know Berk has implemented walls in gromacs 4.0. Check the > new mdp options. Are you sure that you do not want to use peridic > boundary conditions? > > Best, Jochen > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > > -- > ************************************************ > Dr. Jochen Hub > Max Planck Institute for Biophysical Chemistry > Computational biomolecular dynamics group > Am Fassberg 11 > D-37077 Goettingen, Germany > Email: jhub[at]gwdg.de > Tel.: +49 (0)551 201-2312 > ************************************************ > _______________________________________________ > gmx-users mailing list [email protected] > 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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