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

[Tsjerk Wassenaar]

Hi,

You have to make sure that you're molecule doesn't rotate. Otherwise
it will cause direct interactions over the PBC. The same holds true
for large conformational changes.

Cheers,

Tsjerk

On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623