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

[Tsjerk Wassenaar]

You're welcome. Forgot to mention that it comes with an additional
.mdp option (rototr = yes/no). That does break compatibility with
other versions regarding reading .tpr files.

Cheers,

Tsjerk

On Fri, Mar 13, 2009 at 10:48 PM, TJ Piggot <t.piggot at bristol.ac.uk> wrote:
> 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
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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