Re: Question about Generating DCD files with only specified atoms

Date: Thu Dec 22 2005 - 19:36:07 CST

Hello Josh
  i am not quite sure if you can do that while running your simulation,
but there is a nice solution to your problem, use CATDCD. All you need
is an index file which will contain the atom number of your desired
atoms, and the mother dcd file(generated during run). Let me know if you
are not familiar with CATDCD, in that case i can help you.

Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo,ND. 58105.
Phone: 701-231-6491 (Lab)
       701-231-4341 (Res)

> Is it possible to write DCD files (and VELDCD files) during a NAMD run
> where only specified atoms are written. For example, I have a lot of
> water that I need to simulate, but I don't need it at all for analysis
> purposes. Can I not write the water in the DCD files so that the files
> will be smaller?
> Thanks.
> Josh
> --------------------------------------------------
> Joshua D. Moore
> Graduate Student
> North Carolina State University
> Department of Chemical and Biomolecular Engineering
> Box 7905 Centennial Campus
> Engineering Building I
> 911 Partners Way
> Raleigh, NC 27695-7905
> Phone: (919) 513-2051
> Fax: (919) 513-2470
> Email:
> --------------------------------------------------

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