Steven Neumann wrote:
Thank you Justin. I run my pulling using two force constant for pulling.
K1=100 and K1=200
Please, see attached plots of force vs time. Is there any criteria to
adjust pulling constant? Would you suggest running it for a longer time?
I know of no systematic study for choosing a force constant. Guessing wildly at
what's going on, I'd say you need longer simulations as it appears you have only
just caused dissociation towards the end of the 500 ps.
-Justin
Steven
On Mon, Feb 13, 2012 at 1:11 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
Dear Gmx Users,
Is it always required to restrained positions of the protein
while pulling your ligand? My system is made of 10 ligands
attached to my protein surface. I am pulling one of them.
No, it is not required. I assume you've gotten this idea from my
tutorial - the restraints there were used for a very specific
purpose (detailed in the paper linked from the tutorial).
I have just seen trajectory of pulling my ligand without
restraining positions of protein and 9 remaining ligands. My
ligand while pulling also pulled the protein with itself (for 1
nm distance) and then splited. Is is this approach more reliable?
If your goal is umbrella sampling, you need only generate a series
of reasonable starting configurations along a defined reaction
coordinate. The absolute positions are irrelevant; it is the
relative distance that matters.
-Justin
--
==============================__==========
Justin A. Lemkul
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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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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