AMBER Archive (2004)

Subject: Re: AMBER: LES

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Feb 19 2004 - 14:26:21 CST

it _really_ depends on what you're trying to study for your
system. It isn't clear what you're trying to do. The time of the
simulation also depends on what you're trying to do and the system
properties. If you're trying to optimize structure, it can help to
try several annealing protocols and see if the results are sensitive.
With LES, you can look to see if the copies converge at the end of the
annealing, or if they anneal to different conformations.

----- Original Message -----
  From: Petr Jeřábek
  To: amber_at_scripps.edu
  Sent: Thursday, February 19, 2004 1:10 PM
  Subject: AMBER: LES

  dear amber users

  I use the LES method for the protein (haloalkane dehalogenase about 300 aa) with small substrate(trichloropropane), but I dont have many experiences with LES running. I use these temperature parameters for
  heatin phase:

  &wt type='TEMP0', istep1=0, istep2=2500, value1=298.16,
          value2=400.0,
   &end
   &wt type='TEMP0', istep1=2500, istep2=52500, value1=400.0,
          value2=400.0

  and these for cooling phase:

  &wt type='TEMP0', istep1=0, istep2=80000, value1=400.,
          value2=0.0

  So, I would like to know if these temperature parameters are optimal for such system.

  best regards
  Petr
   ----------------------------------------------------
     Petr Jeřábek
     National Centre for Biomolecular Research
     Masaryk University, Faculty of Science
     Kotlarska 2, 611 37 Brno, Czech Republic
   
     phone: +420732338613
     e-mail: rowan_at_chemi.muni.cz
     http://chemi.muni.cz/~rowan
   ----------------------------------------------------

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