From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 03 2013 - 14:38:36 CDT
On Sat, Aug 3, 2013 at 8:24 PM, Joe Janicki <upjjj35_at_gmail.com> wrote:
> I am interested in obtaining the velocities for each atom in my system.
> I used the velDCDfile option in the configuration file and saved the
> velocities at every step. My simulation ran, and I obtained an output file
> with the velocities, saved in the binary DCD format.
> I used "binaryoutput no" in the configuration file, but that appears to only
> work on the final output.
> Is there a way to convert this binary velocity DCD to text? I saw that
> there was a flipbinpdb program, but I'm not sure how to use it/if it will
> help me with what I'm trying to do. I essentially want a plain text file
> with all of the velocities printed out which can be read into a program I
> have written (the details of which are not important).
why go through this conversion ordeal and not simply teach your
program how to read .dcd files?
writing and reading ascii files is slow and wasteful.
the DCD format is simple enough and i am certain that when you do a
little digging on the web, you'll find plenty of code samples at
different level of sophistication. from python/matlab to the VMD
molfile plugin for dcd files, which is probably the fastest reader
short of that, you can use the catdcd utility, which uses the VMD
molfile plugins, to convert your dcds to .xyz format trajectories,
which are pretty much what you are looking for.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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