[gmx-users] Triclinic water box for a protein MD

Lucio Montero lucioric at ibt.unam.mx
Fri Mar 13 19:07:31 CET 2009

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
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