[gmx-users] Protein stability using MARTINI

[XAvier Periole]

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
>> > ============================================
>> >
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
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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
> ============================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
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