Atom Positions during simulation

From: Francisco Castro (Francisco.Castro_at_colorado.edu)
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
(http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/). 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
http://www.ks.uiuc.edu/Research/namd/utilities/ but I keep getting an error
message when I try to unzip it.

 

Thank you very much for your time and consideration

 

Francisco

 

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