Hi,
You can use cpptraj to calculate the radius of gyration from your
trajectory file. Example input:
parm MyTopology.parm7
trajin MyTrajectory.nc
radgyr CA .CA out radgyr.CA.dat
This will give you the radius of gyration of all CA atoms. See the
manual for complete details.
-Dan
On Fri, Mar 4, 2016 at 3:19 PM, Iqbal, Muhammad Sajid <iqbal.uleth.ca> wrote:
> Hi amber community,
>
> I performed MD simulations following the amber tutorial (Running
> minimization and MD in implicit solvent) and would like to see how radius
> of gyration changes over the simulations. Can someone please guide me how I
> can extract this information from my output files?
>
> thank you
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 04 2016 - 14:30:07 PST
