Re: Storing atom coordinates at each time step

From: Richard Wood (
Date: Wed Aug 15 2007 - 19:49:07 CDT

I believe that one can write out a coordinate trajectory in pdb format using NAMD, no? Most programs can do this without the need to write script, because most of us are chemists and NOT programmers. Richard Richard L. Wood, Ph. D. ----- Original Message ---- From: Jeffrey J. Potoff <> To: Audrey Salazar <> Cc: Sent: Wednesday, August 15, 2007 4:48:18 PM Subject: Re: namd-l: Storing atom coordinates at each time step 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? > > > 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. Regards, Jeff -- ====================================================================== 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 ====================================================================== ____________________________________________________________________________________ Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when.

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