Re: [AMBER] Temperature based trajectory in REMD

From: Daniel Roe <>
Date: Tue, 24 Sep 2013 08:56:54 -0600


On Tue, Sep 24, 2013 at 6:44 AM, Gargi Borgohai <> wrote:
> TEMPLIST=`cat temperatures.dat`
> for T in $TEMPLIST ; do
> trajin remd.mdcrd.001 remdtraj remdtrajtemp 267.0
> trajout remd.Ttraj.267

This script as written will give only the trajectory at 267 K. It
should be something like:

trajin remd.mdcrd.001 remdtraj remdtrajtemp $T
trajout remd.Ttraj.$T

FYI you may be interested in trying the 'ensemble' command in cpptraj,
which will sort and process all temperatures at once. For example, the
input to cpptraj in your case would be (no 'for' loop required):

ensemble remd.mdcrd.001
trajout remd.Ttraj

You would obtain trajectory files 'remd.Ttraj.X', where X corresponds
to a position sorted temperature list starting from 0. You can also do
some simple actions on the entire ensemble at once (calculate
distances, rmsds etc).

> While calculating average value of helical fraction
> (averaged over all frames) for each temperature the value is found to be
> near about same for each temperature. And when population of "native state"
> was calculated for each temperature, it was found to decrease with
> increasing temperature (which is expected). But this % of population at the
> lowest temperature (i.e. at 267K) is very small, its about ~10% of the
> total frames of the whole temperature based trajectory (which is obtained
> from remd.Ttraj.267). But this is not expected. I may have done some
> mistake either in finding out temperature based trajectory or in finding
> the population of "native state" at each temperature. Will you please help
> me in choosing the right pathway to calculate the same? This will be a
> great help for me.

Unfortunately there is no easy answer here, and without knowing more
about what your system actually is I can only speculate. Do you have
experimental evidence for what the population should be at 267 K? Also
267 K is getting pretty cold, and some proteins do undergo a
phenomenon known as "cold denaturation" (although usually a
temperatures a little colder). If you started your REMD simulation
with a conformation other than native it could be that you haven't run
long enough and your ensemble simply hasn't converged. Do you have at
least one other independent REMD simulation that gives similar

Hope this helps,


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 24 2013 - 08:00:03 PDT
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