Re: Selected cofactor in final output

From: Giacomo Fiorin (
Date: Fri Nov 15 2019 - 13:14:29 CST

To the best of my knowledge DCD files are written for the entire system

But you can always use a post-processing tool like catdcd to write out only
a portion of the atoms, after which you can delete the complete trajectory
if you don't need it and want to save space.


On Fri, Nov 15, 2019 at 9:53 AM Aashish Bhatt <>

> Dear Namd uses
> I want to study terahertz spectra in some cofactor present in the my
> protein.
> My protein is 551 aa residue long. I want to perform 10ns simulation of
> where 1fs is timestep.
> Is it possible to save only selected cofactor velocity coordinates in dcd
> file at that time where classical md simulation is run.
> Best regards
> Aashish Bhatt

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD

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