Re: amber-developers: REMD and PTRAJ manuals

From: Daniel Roe <>
Date: Mon, 21 Apr 2008 10:29:42 -0400


Ptraj can indeed read the new REMD format and process whatever temperature
you want. In order to process the data at a given temperature, the usage is:

trajin <trajectory> remdtraj remdtrajtemp <TEMP>

where <trajectory> is the new format REMD trajectory file that corresponds
to the lowest number replica, with an integer extension of format XXX (e.g.
000, 001 etc - should also recognize the .gz extension, e.g. 000.gz, 001.gz)
and <TEMP> is the temperature of the data you want to analyze. The code will
then look for all replica trajectories and process them all at the same
time, only using data at the temperature you specify. At this point you
could use a trajout command to write an amber temperature trajectory.

If the 'remdtraj' keyword is not specified then the trajectory is treated
simply as a replica trajectory.

This information should certainly be in the ptraj manual - I apologize for
not making sure it was in there.


On Mon, Apr 21, 2008 at 10:17 AM, Gustavo Seabra <>

> Hi All,
> I was looking at the amber10 ( and
> ambertools ( manuals published,
> and noticed that some information seems to be missing:
> The Amber10 manual mentions in the REMD section, that the output files
> in Amber10 differ from previous versions in that they are organized by
> replica, not by temperature, and that ptraj will be able to read
> trajectories in this new format. Although nothing is mentioned about
> that, I imagine ptraj should also be able to analyze those files by
> temperature itself, or at least to write new "by-temperature
> trajectories", which can later be analyzed in ptraj again. The only
> issue is that the ptraj session in the ambertools manual is apparently
> missing the instructions to deal with REMD output files. Is this
> information really supposed to be part of ptraj's manual, or should it
> be in the Amber manual? (It's not present in either)
> Gustavo.

Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741
Received on Wed Apr 23 2008 - 06:07:27 PDT
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