From: Audrey Salazar (alsalazar_at_northwestern.edu)
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
-- 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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