AMBER Archive (2003)

Subject: AMBER: please let me know if this is correct

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Jul 28 2003 - 08:58:55 CDT

Dear Amber users,
  During a simulation with ntt=1 and tautp
the velocities are scaled proportionally per time step from v to lambda*v
where
 lambda=1 + (delta)t/2*tautp(T0/T-1) and tautp (from the namelist is
taken in this equation by sander).
Please let me know if this is correct or not.

Trying to swich to NAMD
The equation given in the XPLOR program:
bi=biT(T0/T-1)
where bi is the friction coefficient applied by the program and biT is
the coefficient that we have to supply in tCoupleFile (please let me
know if this is correct ...this is just my thought)...so I fugured out
comparing the 2 eq. that:

biT=(delta)t/2*tautp where (delta)t is the timestep.

so for an equilibration in amber with (delta)t=0.001 and ntt=1 and tautp=0.2
I came up with a biT=0.0025 that has to be set in the tCoupleFile for
running a similar simulation using NAMD.

Please let me know if my assumptions were correct and if this makes
sense...I know it might be trash but somehow I need to run NAMD on The
cluster that I am using now because there is a problem with Amber and I
a have a "time pressure problem" and I am trying to use the same
protocol for the 2 programs.
Thanks a lot for understanding this,
Best wishes,
vlad 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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