Re: concatenating two or more dcd files

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

Hi,

> 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, ...

Cheers,

Marc

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