AMBER Archive (2006)

Subject: Re: AMBER: question on protein folding simulation

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Fri Dec 01 2006 - 13:56:06 CST

I donot know whether I am right. Can you di the
simulation without water box, and after it is
partially folded, you add a water box? Maybe this
method will be much better.

Best regards.

Fenghui Fan

--- Noriaki Okimoto <okimoto_at_gsc.riken.jp> wrote:

> Hi amber users,
>
> I am going to try protein folding simulations. My
> target protein consists of 35 amino acid residues.
> At first, I am going to perform folding simulations
> from extended structure with a periodic boundary
> system. After it will collapse and pack compactly in
> the simulation, I would like to reduce the system
> size (that is, reduce number of water molecules in
> the system) and continue to perform the folding
> simulation from the reduced system, because the
> system size with the extended structure is very
> large. In reducing system size, I would like to
> treat hydrated water molecules around the peptide
> with those velocities obtained from simulations of
> the extended peptide. But I have no proper and
> cleaver idea on reducing the system size.
> One idea is that new water molecules are generated
> by using leap module, and then those only new water
> molecules are equilibrated by short simulation
> (several tens of pico seconds) with restraining
> motion of peptide, to obtain start system for
> continuous folding simulation. Is this way proper?
>
> Does anybody could help me and give the advice to
> reduce the periodic system size for protein folding
> simulation.
>
> Thank you in advance.
>
> Noriaki Okimoto
>
>
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