Re: unit of output velocity

From: Satish Kumar <>
Date: Fri, 6 Jun 2003 21:55:58 +0530

check this extract...

.......Amber internally uses lengths in angstroms, masses in atomic mass
units, and energies in kcal/mol. This means that the unit of time is
1/20.455 ps. Since the set of units is internally consistent, you should be
able to compute the kinetic energy in the "normal" fashion:

  KE(in kcal/mol) = 1/2 sum mv**2

where the masses are in amu and the velocities are from the program.
Note, however, that the velocities stored in the restart file are the
velocities at a time 0.5(dt) before the time of coordinate (since a
"leap-frog" integration scheme is being used. When amber actually prints
kinetic energies, it estimates the velocities at the current time [by
averaging those at t - 0.5(dt) and t + 0.5(dt)]. So your kinetic energies
won't exactly match those printed unless you do something equivalent.

VDW parameters: R* is in Angstroms, epsilon in kcal/mol. .....

Satish Kumar.M
Bioinformatics Group,
National PARAM Super Computing Facility Bldg
Centre for Devlopment of Advanced Computing,

----- Original Message -----
From: "Yuguang Mu" <>
To: <>
Sent: Friday, June 06, 2003 9:03 PM
Subject: unit of output velocity

> Dear all,
> Who knows the unit of output velocity in AMBER6 ?
> Thanks in advance.
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
Received on Fri Jun 06 2003 - 17:53:01 PDT
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