Re: amber-developers: REMD and PTRAJ manuals

From: Carlos Simmerling <>
Date: Wed, 23 Apr 2008 14:01:15 -0400

I have a REMD tutorial that I am just finishing updating for Amber 10, should
be done next week. It will go through this ptraj analysis and give some sample

On Wed, Apr 23, 2008 at 12:12 PM, David A. Case <> wrote:
> 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?
> ...thx...dac

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
Received on Sun Apr 27 2008 - 06:07:18 PDT
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