Anirban Ghosh wrote:
Hi ALL,
I want to do a MD simulation by restraining (freezing) the helical
portions and allowing only the loop regions to move. I tried doing this
by applying heavy restrain on the helical residues by generating a .itp
file with the "genrestr" command with an index file containing the
desired residue numbers. However during the simulation I am finding that
the entire protein is moving. Am I doing anything wrong? Or is there any
other way to freeze a portion of a protein? Any suggestion is welcome.
thanks a lot in advance.
If your protein is still moving, then you aren't correctly applying your
position restraints. Without seeing your topology and .mdp file, there's no way
to know what you're doing wrong.
You can also use the freezegrps option in the .mdp file, but then you also have
to make sure you're using the appropriate energygrp_excl, etc. It is generally
much easier to apply position restraints.
-Justin
Regards,
Anirban
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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