Re: [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets

From: Daniel Roe <>
Date: Fri, 21 Jan 2022 18:46:28 -0500

Just a quick follow-up: I just found and fixed an issue with
clustering when using a previously generated pairwise distance matrix.
Details here:

If you're clustering with cpptraj it's probably worth it to update.


On Tue, Jan 18, 2022 at 8:21 PM Daniel Roe <> wrote:
> Hi all,
> Just FYI I’ve just fixed a performance issue in some of the post-clustering steps in cpptraj (summary, best representative frames calc, silhouette etc) that in particular would impact clustering runs on high #s of frames (e.g. 100,000 frames with sieving). The fixes are in version 6.2.0 (GitHub). See
> for more details.
> -Dan

AMBER mailing list
Received on Fri Jan 21 2022 - 16:00:04 PST
Custom Search