Atom Positions during simulation

From: Francisco Castro (
Date: Wed Dec 14 2005 - 16:27:12 CST

Dear NAMD users,


I am a new NAMD user and I have some questions regarding the atom positions.


I have started by following the example given in the NAMD website tutorial
section called Interactive Molecular Dynamics
( The software runs
perfectly and I can see the simulation via VMD.


My question is: How can I obtain the location or the coordinates x, y and z
of the atoms for every time step during the simulation?

After I run the simulation there are three output files with extensions
COOR, VEL and XSC but I have not been able to open those, what software do I
need to do that?


I was thinking on using the Matlab script posted on but I keep getting an error
message when I try to unzip it.


Thank you very much for your time and consideration




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