Hi, You have to make sure that you're molecule doesn't rotate. Otherwise it will cause direct interactions over the PBC. The same holds true for large conformational changes.
Cheers, Tsjerk On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul <[email protected]> wrote: > > > Lucio Montero wrote: >> >> I want to simulate a protein complex using a triclinic box, because it >> reduce my system size in 60%, and consequently the computing time. I have >> read that using a triclinic box can give problems for a long MD if the >> peptide has a whirl, but I don´t know if it is a problem for a complex of ~ >> 530 aa (protein 1: 376 aa, protein 2: 132 aa, protein 3: 20 aa, complex size >> 64x64x104 Angstroms) surrounded by 12 Ângstroms of water. I want to run the >> MD simulating 20 ns. > > What problems have you read about? Can you cite a source so we know what > you're talking about? > > -Justin > >> Best regards, >> Lucio Montero >> >> -------------------------------------------------------------------------------------------------------------------------------- >> Lucio Ricardo Montero Valenzuela >> Laboratorio del Dr. Federico Sánchez >> Ext. 27666 >> Departamento de Biología Molecular de Plantas >> Instituto de Biotecnología, UNAM >> Cuernavaca, Morelos, 62210 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
