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

[Justin A. Lemkul]

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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-- 
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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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