amber-developers: REMD and PTRAJ manuals

From: Gustavo Seabra <>
Date: Mon, 21 Apr 2008 10:17:06 -0400

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)

Received on Wed Apr 23 2008 - 06:07:27 PDT
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