AMBER Archive (2009)

Subject: [AMBER] rescaling velocities

From: abi ghanem (
Date: Thu Jun 04 2009 - 11:39:02 CDT

I just have a question about the rescaling of velocities,
I am using the berendsen algoritm with a TAUPT of 5ps.

This is the input for my dynamic:

    imin=0, ntx=7, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
    ntf=2, ntc=2,
    ntb=2, ntp=1, tautp=5.0, taup=5.0,
    nstlim=100000, t=0.0, dt=0.002,
    irest=1, nmropt=1
&wt type='END', &end

Is the velocity rescaled in my case ? if yes, how often?

I didn't write a .mdvel, but i want to extarct the velocity at each
step, is it possible and how?

Thanks a lot for your help,

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