Re: Storing atom coordinates at each time step

From: Jason O'Young (
Date: Wed Aug 15 2007 - 17:21:28 CDT

Hi Audrey.

The coordinates are stored in the DCD file in a binary format (this
is why it looks like junk).

You can visualize the data with VMD.

If I am not mistaken, I believe there are some tools/plugins buried
on the NAMD site to extract coordinates from a DCD and calculate the
center of mass over time.


On 15-Aug-07, at 4:03 PM, Audrey Salazar wrote:

> Hello,
> 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
> --
> 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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