From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
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?
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 jpotoff_at_chem1.eng.wayne.edu 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 http://potoff1.eng.wayne.edu ======================================================================
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