Re: concatenating two or more dcd files

From: Marc Q. Ma (
Date: Mon Apr 18 2005 - 12:13:51 CDT


> I am loading several dcd files from MD simulations. If I have a file
> that goes, for example, from timestep 1 to 10000, and another file,
> which is a continuation run of the first one, from timestep 9000 to
> 15000, what happens when I load one and then the other file? I would
> like a trajectory that goeas from 1 to 15000 (without duplicating the
> frames corresponding to 9000-10000). Are the frames corresponding to

You can first load the first 1 to 10000 frames, then delete the last
1000 frames, then load the 9000-15000 frames. Now you have loaded
frames from 1 to 15000 without duplicates.

To do this, choose Molecule -> Delete Frames ...

> timesteps 9000-10000 from the first dcd file overwritten when I load
> the
> files in VMD? or are ALL frames loaded sequentially? What is the best

NO. You will get duplicates in the movies.

> way of concatenating several dcd files?

If you have an implementation of DCD reader and a DCD writer, it does
not matter what languages you use, you can easily manipulate these
files such as concat two files, spit out the last frame, remove some
frames, ...



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