Re: [AMBER] cpptraj frames clustering limit

From: Jason Swails <>
Date: Wed, 12 Aug 2015 09:59:58 -0400

On Wed, Aug 12, 2015 at 9:46 AM, Gaurao Dhoke <> wrote:

> Hello Amber Users,
> I am using cpptraj of Amber 14 for some analysis. I have a very long
> trajectory (more than 50000 frames).
> I have found that cpptraj is not able to process long trajectory for
> analysis.

​What makes you arrive at this conclusion?

> Do anyone have an idea how many maximum frames cpptraj can process?

​There is no limit. And in fact, for most trajectory analyses, cpptraj
only stores a single frame in memory at a time, meaning that it can process
*very* long trajectories that won't fit entirely in system memory.

That said, *some* analyses require that all frames be accessible in memory
-- like 2D-RMSD, clustering, etc. In this case, the number of frames that
can be analyzed is limited by the amount of RAM in your computer.

> ​​
> Is there any way to increase this limit?

​Since you're doing clustering, either your system is running out of memory
or you are expecting a calculation that may take hours or days to finish
much faster than that (so you think it's hanging, when in fact it's still
working). You haven't provided enough information about what happened for
me to know for sure.

If you are actually running out of memory, your choices are either use a
machine that has more RAM, or use the "sieve" option, which will generate
the clusters based on a reduced number of frames, and then assign *all* of
the frames to that cluster. More details are available in the manual.

Also, I would highly recommend upgrading to AmberTools 15 if you haven't
already (if you have Amber 14, you can do this with a simple
"./update_amber --upgrade" command).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Aug 12 2015 - 07:30:03 PDT
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