Re: Storing atom coordinates at each time step

From: Jeffrey J. Potoff (
Date: Wed Aug 15 2007 - 15:48:18 CDT

Audrey Salazar wrote:

>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?
Dear Audrey,
    The *.dcd file contains the information you are after. The data are
stored in binary format to reduce the amount of disk space used. You
can read the dcd file in VMD and save the coordinates in a human
readable format via "File" and "save coordinates". With a little bit of
work, I'm sure you could automate this process.

>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?
Anything is possible if you're willing to write some code to do it. In
VMD, this could be done via the tcl scripting language.


Jeffrey J. Potoff               
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815

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