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. 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
