Re: Storing atom coordinates at each time step

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Aug 15 2007 - 20:30:01 CDT

You can also use catdcd (
http://www.ks.uiuc.edu/Development/MDTools/catdcd/) for this conversion:

catdcd -s originalfile.pdb -stype pdb -o trajectory.pdb -otype pdb
dcdfile.dcd

NAMD doesn't write ascii trajectory files because they really get rather
wasteful if you're doing a long run; however, as you can see there are a
number of ways of easily obtaining them from a dcd. Hopefully a one line
command doesn't constitute a script...

By the way, just as an example (since Audrey asked), a script to print
the center of mass to a file might look like:

set ofile [open "filename" "w"]
set sel [atomselect top all]
for {set i 0} {$i < [molinfo top get numframes]} {incr i} {
  $sel frame $i
  puts $ofile [measure center $sel weight mass
}

$sel delete
close $ofile

(with some selection you want in place of all)

Peter

Richard Wood wrote:
> 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.
> rwoodphd_at_yahoo.com
>
>
> ----- Original Message ----
> From: Jeffrey J. Potoff <jpotoff_at_chem1.eng.wayne.edu>
> To: Audrey Salazar <alsalazar_at_northwestern.edu>
> Cc: namd-l_at_ks.uiuc.edu
> 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 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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