[AMBER] Temperature based trajectory in REMD

From: Gargi Borgohai <gargib2011.gmail.com>
Date: Tue, 24 Sep 2013 18:14:43 +0530

Dear AMBER Users,

I have a query about postprocessing data obtained from REMD simulation. I
have used a system consisting of a peptide and water and run an REMD
simulation. To obain temperature based trajectories I used the following
ptraj script in AMBER12

TEMPLIST=`cat temperatures.dat`

for T in $TEMPLIST ; do

trajin remd.mdcrd.001 remdtraj remdtrajtemp 267.0
trajout remd.Ttraj.267

After running this script , "remd.Ttraj.267" is generated containing same
number of frames as with each replica based trajectory (viz.
remd.mdcrd.001). 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.

With regards..

Gargi Borgohain
PhD Student
IIT Guwahati
AMBER mailing list
Received on Tue Sep 24 2013 - 06:00:03 PDT
Custom Search