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

[Tsjerk Wassenaar]

Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an
optimally packed system and simulate it with the Gromacs 3.3.1 version
you can download from
http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.3.1-rtc.tgz
That version of gromacs has the roto-translational constraints
implemented that were developed by Andrea Amadei.
Mind that the server is fresh :) The paper is about to be submitted.
Unfortunately I haven't had time to dig into the GMX 4 code to
implement the rotational constraints yet. I wouldn't want to
compromise the performance :S

Cheers,

Tsjerk

On Fri, Mar 13, 2009 at 8:26 PM, TJ Piggot <t.piggot at bristol.ac.uk> wrote:
> 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.
>
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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