**From:** Blake Charlebois (*bdc_at_mie.utoronto.ca*)

**Date:** Thu Sep 02 2004 - 08:21:34 CDT

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Eric,

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?

Blake

-----Original Message-----

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf

Of Eric Cyr

Sent: August 31, 2004 4:45 PM

To: namd-l_at_ks.uiuc.edu

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

suspected

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

what

the difference could possibly be. Any suggestions?

Thanks for any help

Eric

**Next message:**Edward Patrick Obrien: "Re: Questions on periodic boundary condition"**Previous message:**ying xiong: "calculate the binding energy or binding free energy?"**In reply to:**Eric Cyr: "Calculation of velocities"**Next in thread:**Eric Cyr: "Re: Calculation of velocities"**Reply:**Eric Cyr: "Re: Calculation of velocities"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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