AMBER Archive (2004)

Subject: AMBER: LES

From: Petr Jeřábek (
Date: Thu Feb 19 2004 - 12:10:50 CST

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,
 &wt type='TEMP0', istep1=2500, istep2=52500, value1=400.0,

and these for cooling phase:

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

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

best regards
   Petr Jeřábek
   National Centre for Biomolecular Research
   Masaryk University, Faculty of Science
   Kotlarska 2, 611 37 Brno, Czech Republic
   phone: +420732338613

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