Re: [AMBER] Calculate average property

From: Daniel Roe <>
Date: Tue, 17 Sep 2013 09:08:48 -0600


Just to add to what Jason said, if you do end up deciding on a metric
(such as an RMSD cutoff) you can run the calculation on the entire
REMD ensemble at once (with cpptraj) by reading in your replica
trajectories with the ensemble command. For example, say you have 4
temperature replica trajectories named rem.1, rem.2, rem.3, and rem.4;
you can read and calculate RMSD for the sorted ensemble like so:

reference folded.rst7
ensemble rem.1
rmsd reference .CA out rmsd.dat

After the calculation rmsd.dat will have 5 columns; the #Frame column,
followed by 1 column for the RMSD at each temperature (increasing).


On Tue, Sep 17, 2013 at 8:24 AM, Jason Swails <> wrote:
> On Tue, Sep 17, 2013 at 7:05 AM, Gargi Borgohai <>wrote:
>> Dear amber Users,
>> I want to calculate average value of 'folded fraction' (at a particular
>> temperature) of a protein which is simulated by REMD method. For this
>> purpose temperature based trajectories are generated first. After that is
>> it necessary to take average over all the frames at that particular
>> temperature?
> As opposed to what alternative? I'm a bit confused here. If you want the
> "fraction folded", then you need to come up with some metric for deciding
> whether a protein is 'folded' or not, and you count up the number of
> snapshots that are 'folded' and divide that by the total number of
> snapshots you are considering.
> Some people consider all snapshots; others omit some for one reason or
> another -- it all depends on what questions you want to ask or what you're
> hoping to learn.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Sep 17 2013 - 08:30:02 PDT
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