Storing atom coordinates at each time step

From: Audrey Salazar (
Date: Wed Aug 15 2007 - 15:03:37 CDT

I am a first year graduate student modeling nucleic acids in NAMD.
For every time step, NAMD, like all MD programs, calculates the
coordinates of each atom for each time step.

** Is there a way that I store this information in a file?

I have looked in all the files that my .conf file specifies to output:
.vel, .coor, .dcd (these three files are illegible), .xst, and .xsc.

Do any of these files contain the information that I seek? If the
information is contained in the illegible files, how can I read them?

For long nucleic acid chains, writing these coordinates to a very
large file will be very cumbersome.

**Is there a way that I could store the coordinates of the center of
mass of parts of the chain at every time step to file instead?

I would appreciate any guidance that the NAMD community might be able
to provide.

Thank you.


Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering      Phone: 847.491.2188
Northwestern University
Evanston, IL USA

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