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
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--
========================================
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
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