Re: amber-developers: REMD and PTRAJ manuals

From: David A. Case <>
Date: Wed, 23 Apr 2008 09:12:18 -0700

On Mon, Apr 21, 2008, Daniel Roe wrote:
> 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.

Thanks. I've put this information into amber11/doc/AmberTools.lyx, so it will
be available at the next release.

Do replica exchange runs automatically create the right sort of trajectory
to be used in this way? Is there an example in the manual of what to do, or
(better) a tutorial that runs replica exchange with the new procedures?

Received on Sun Apr 27 2008 - 06:07:15 PDT
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