AMBER Archive (2006)

Subject: AMBER: question on protein folding simulation

From: Noriaki Okimoto (okimoto_at_gsc.riken.jp)
Date: Fri Dec 01 2006 - 06:01:27 CST

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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