Re: Question about Generating DCD files with only specified atoms

From: Joshua D. Moore (
Date: Thu Dec 22 2005 - 22:23:02 CST

Hi Pijush and Sterling,

I do use catdcd with the index file. It is very useful, and I guess I can
just do this. However, I wanted something that would actually write the
dcd files I wanted. I can easily include this post processing with catdcd
in a script, but I want to refrain from writing the large files in the
first place.

By the way, Pijush, I asked you about the catdcd 4.0 source. It is in the
CVS plugin source tree if anyone ever needs to find it. I also remembered
where I got the binaries now. They are in the vmd_plugin library updates
for many architectures.

Thanks again guys. If anyone knows how to do generate dcd files with namd
runs with only specified atoms, I still haven't figured it out, but I
guess I can stick with the post processing with catdcd for now.

Maybe if this option doesn't already exist, it could be added to a future
version of NAMD?


On Thu, December 22, 2005 10:17 pm, Sterling Paramore wrote:
> I'm not sure if you can do it within NAMD, but you could always use the
> "index file" option of catdcd (remember than the first atom is number 0)
> and create a new dcd file without the water.
> -Sterling
> Joshua D. Moore wrote:
>>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?
>>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

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

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