RE: Calculation of velocities

From: Blake Charlebois (
Date: Thu Sep 02 2004 - 08:21:34 CDT


I am no expert, but I expect using the Verlet algorithm to compute
velocities should give you numbers quite close to those computed by NAMD
(which uses the velocity Verlet algorithm, if I remember correctly).

Are all three velocity components out by approximately the same factor at
every timestep? How much does this factor vary?

Would you consider posting the relevant lines from your configuration file?


-----Original Message-----
From: [] On Behalf
Of Eric Cyr
Sent: August 31, 2004 4:45 PM
Subject: namd-l: Calculation of velocities

I need to calculate particle velocities in the applied forces scripting
interface, since no "loadvelocities" command exists. I've been trying
to use a centered difference (x(n+1) - x(n-1))/(2dt). However, I
my answers were incorrect. So I had NAMD dump ASCII restart files
and looked at the values calculated by them. Even when accounting
for the PDBVELFACTOR the values I calculated for the velocities were
about 1/50th of what they should be. I've been trying to figure out
the difference could possibly be. Any suggestions?

Thanks for any help

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