Liu, Liang wrote:
How's position restraint? If the force constant is reduced (reduce the
number in posre.itp ?), the simulation will lead to more flexible structure?
Position restraints are inherent inhibition to structural sampling. Their
intent is to prevent the protein (or whatever restrained molecule) from changing
too much. Of course, it can change since it's only a harmonic potential, but if
you're looking for better sampling then I would turn off any form of position
restraints.
-Justin
On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Liu, Liang wrote:
Thanks.
Will the constrain help?
Bond constraints? Well, in general, they're useful, and likely
necessary at high temperature to keep your system stable. Please be
more specific.
-Justin
On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Liu, Liang wrote:
Hi, all,
I am trying to use Gromacs to obtain structural ensembles
around
native structures (PDB structures).
However the simulated structures are always very close to the
initial one, with RMSD < 0.2.
I am wondering how to obtain large-RMSD structures? Thanks.
Large RMSD values would indicate non-native structures, which
doesn't sound like what you're looking for. If your goal is
simply
enhanced sampling, try REMD.
-Justin
-- ==============================____==========
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==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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