AMBER Archive (2009)

Subject: Re: [AMBER] combining MD runs for post-MD analysis

From: case (
Date: Sun Sep 20 2009 - 20:35:08 CDT

On Mon, Sep 21, 2009, Jeff Yeo wrote:
> Currently I have 2 separate sets of results (e.g. mdcrd, etc) from those
> two MD runs. Is there a way to combine the separate sets of results
> before I start my post-MD analyses (e.g. RMSD, MM/PBSA, etc)? Will cat
> md1.mdcrd md2.mdcrd work?

Just "cat" won't work. Use ptraj, with this sort of input:

trajin MD1.crd (or whatever its name is)
trajin MD2.crd
trajout MD1-2.crd (see manual for optional arguments, especially "nobox")

Note, however, that there probably is no real need to do this. You can just
have several "trajin" lines (as above), and substitute whatever analysis you
need for the "trajout" line above.

...good luck...dac

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