AMBER Archive (2004)

Subject: RE: AMBER: algorithm used in AMBER

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jan 02 2004 - 07:05:13 CST

Dear Hungie

Amber uses the Leap-Frog Algorithm where:

The kinetic energies at time t are either obtained by considering the
kinetic energy at time t-dt/2 and t+dt/2 (Amber 4,5,6):

Approx KE(t) = [ KE(t-dt/2) + KE(t+dt/2) ]/2

For amber7 the kinetic energies at time t are obtained in a 'technically'
better way by doing a half time step update to find the velocities at time t
from the data at t-dt/2 and then using these velocities to calculate the
kinetic energy. Note: These velocities are ONLY used for calculating the
kinetic energy they do not affect the trajectory.

I hope this helps
All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
A. Hungie
Sent: 02 January 2004 02:07
To: amber_at_scripps.edu
Subject: AMBER: algorithm used in AMBER

Dear All,

Could you please tell me what algorithm is used in AMBER (MD simulations) to

solve Newton's equation, Verlet or Leap-Frog or another?

Many thanks in advance

Hungie

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