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

[Lucio Montero]

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

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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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