AMBER Archive (2004)

Subject: AMBER: LES

From: Petr Jeřábek (rowan_at_chemi.muni.cz)
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,
        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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