Re: protein folding

From: Axel Kohlmeyer (
Date: Fri Jul 10 2009 - 07:48:02 CDT

On Fri, 2009-07-10 at 11:00 +0300, doty alexiou wrote:

> Hi.I am running an NAMD simulation of a protein(folding process) using
> the extended martini foce field.The simulation has run about 70-80
> ns(323 k,timestep 10,PBC,in water,RMSD is about 18 till now).Up until
> now,there is no sign of the expected secondary structure of the
> protein.Is there any suggestion about what could be wrong or if i
> should expect it longer?Thank u.

do you have any proof that the martini force field _can_ fold proteins?

the 2008 monticelli paper explicitly states that the secondary structure
of proteins is not at all modeled, but used as input parameter and then
kept fixed. so in my opinion you are currently wasting your time and
that of your computer.


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Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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