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 <[email protected]>
Date: Monday, September 6, 2010 14:06
Subject: [gmx-users] Protein stability using MARTINI
To: Discussion list for GROMACS users <[email protected]>
> 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: [email protected]
> ============================================
>
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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: [email protected]
============================================
--
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