Re: How to write different DCD files for separate MD runs in one simulation?

From: Peter Freddolino (
Date: Tue Apr 15 2008 - 14:07:03 CDT

Hi Yinglong,
there isn't a convenient way to split the dcd file in the middle of the
simulation; the file handle is opened at the start, headers are written,
and then it is appened to throughout the simulation. If you want to
split up your files like this, it would be far simpler to postprocess
them with catdcd rather than writing them to separate files on the fly.
With that said, if you must modify things, you can find the functions
used for dcd writing in Output.C.


Yinglong Miao wrote:
> Hi,
> I have a question about how to write different DCD files for separate
> runs in one NAMD simulation. In one of my simulations, I tried the
> following:
> DCDfile ${outputname}_1.dcd
> run 200
> DCDfile ${outputname}_2.dcd
> run 200
> But it turned out that I cannot name different DCD files for the two
> run parts like this:
> TCL: Setting parameter DCDfile to 1cwp-vmd-H-out_2.dcd
> FATAL ERROR: Setting parameter DCDfile from script failed!
> So I am writing to check whether NAMD 2.6 provides such an option. If
> so, what did I do wrong? If not, can anybody tell me how to modify the
> source code easily for my purpose? Your help will be greatly appreciated.
> Thanks,
> Long
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981

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