Re: [AMBER] cpptraj on pH-REMD

From: Jason Swails <>
Date: Wed, 24 Aug 2016 22:34:16 -0400

Unless your trajectories are named with incrementing numbers coming at the
end of the trajectories, you need to use "trajnames" in the trajin command
to do this.

Note that (since I was lazy and wanted to get pH-REMD working quickly
several years ago) the pH is stored in trajectories as the "temperature",
specifically so that pH-REMD files could take advantage of existing tools
for processing T-REMD files. But your trajin line should look something
like this:

trajin trajnames,,...

Also, I suggest consulting some of the REMD tutorials to try and understand
how to analyze REMD trajectories (which is a little different than
analyzing "normal" trajectories).


On Wed, Aug 24, 2016 at 7:19 AM, Elisa Pieri <>

> Hi,
> I want to rebuild the trajectories from 12 pH-REMD .nc files named
> (where X ranges from 01 to 12). I have to say that I don't get cpptraj so
> much. Can anybody tell me the command to achieve this goal?
> Thank you in advance,
> Elisa
> _______________________________________________
> AMBER mailing list

Jason M. Swails
AMBER mailing list
Received on Wed Aug 24 2016 - 20:00:02 PDT
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