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

[TJ Piggot]

You might want to try a rombic dodecahedron box (an option in editconf).

Or you can run the simulation using a triclinic box hoping the images don't 
interact and then check after the simulation has finished using g_mindist 
-pi on the trajectory, bearing in mind if they do then you will have wasted 
a lot of time.

If you do want to use a triclinic box having a larger amount of water 
surrounding the complex may be advisable as this makes images interacting 
less likely

Tom

--On Friday, March 13, 2009 20:10:05 +0100 Tsjerk Wassenaar 
<tsjerkw at gmail.com> wrote:

> 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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>>
>> --
>> ========================================
>>
>> 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
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.