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

[TJ Piggot]

This looks great thanks, had meant to try and implement something like 
these restraints for ages but never got round to it, you know how it is ...

Tom

--On 13 March 2009 21:06 +0100 Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.