[gmx-users] Protein stability using MARTINI

[Tsjerk Wassenaar]

Hey,

It might also be related to the PBC, with gromacs not writing whole
molecules anymore. Maybe a link to a picture would be good, showing
protein beads spheres, together with the (triclinic) unit cell.

Cheers,

Tsjerk

On Mon, Sep 6, 2010 at 12:05 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> Dear Itamar,
> If your problem is not a bond length definition in VMD (which
> you can overcome by using "dynamic bonds", although it is not
> perfect) you may have a problem in your topology.
> The way you describe your problem (groups of bids moving freely)
> suggests that you do have a topology problem.
> XAvier.
> On Sep 6, 2010, at 11:52 AM, Itamar Kass wrote:
>
> Thanks Mark for the replay,
> I used VDW presentation to over come it.
> Best,
> Itamar
>
> On 6/09/2010 6:33 PM, Mark Abraham wrote:
>
> ----- Original Message -----
> From: Itamar Kass <itamar.kass at monash.edu>
> Date: Monday, September 6, 2010 14:06
> Subject: [gmx-users] Protein stability using MARTINI
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>>  HI all,
>>
>> I am simulating a protein in water using the MARTINI (CG) force
>> field. My protein composed of few alpha-helices and a big tail
>> (~50AA) which is random coiled. I have built the simulation
>> system according to the procedure at
>> http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-
>> water .
>>
>> After a 10ns simulation, I have visualised the system using VMD.
>> It seems like the protein had dismantled to amino acids. I see
>> groups of bids moving freely in the system.
>
> I'm not sure what you mean here, but it seems likely that VMD's heuristics
> for guessing where bonds between atoms might exist aren't going to work well
> for a coarse-grained protein. There's probably a standard solution, for
> which you should Google :-)
>
> Mark
>
>>
>> Any idea of the problem? Any idea how to fix it?
>>
>> PS I don't want to use elastic network for the random coil tail,
>> as I wish to capture as much conformation as possible.
>>
>> Thanks in advance,
>> Itamar.
>>
>> --
>>
>>
>> "In theory, there is no difference between theory and practice.
>> But, in practice, there is." - Jan L.A. van de Snepscheut
>>
>> ===========================================
>> | Itamar Kass, Ph.D.
>> | Postdoctoral Research Fellow
>> |
>> | Department of Biochemistry and Molecular Biology
>> | Building 77 Clayton Campus
>> | Wellington Road
>> | Monash University,
>> | Victoria 3800
>> | Australia
>> |
>> | Tel: +61 3 9902 9376
>> | Fax: +61 3 9902 9500
>> | E-mail: Itamar.Kass at monash.edu
>> ============================================
>>
>> --
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>
> --
>
>
> "In theory, there is no difference between theory and practice. But, in
> practice, there is." - Jan L.A. van de Snepscheut
>
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: Itamar.Kass at monash.edu
> ============================================
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands