Re: Question about Generating DCD files with only specified atoms

From: Sterling Paramore (
Date: Thu Dec 22 2005 - 21:17:41 CST

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.


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

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