Calculation of velocities

From: Eric Cyr (ericcyr_at_uiuc.edu)
Date: Tue Aug 31 2004 - 15:44:47 CDT

• Next message: John Stone: "Re: vmd-l: rmsd problem"
• Previous message: lc_at_chem.au.dk: "estradiol"
• Next in thread: Blake Charlebois: "RE: Calculation of velocities"
• Reply: Blake Charlebois: "RE: Calculation of velocities"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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: John Stone: "Re: vmd-l: rmsd problem"
• Previous message: lc_at_chem.au.dk: "estradiol"
• Next in thread: Blake Charlebois: "RE: Calculation of velocities"
• Reply: Blake Charlebois: "RE: Calculation of velocities"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:50 CST