Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Steven Neumann wrote:
Dear Justin and Gmx Users,
I run a pulling of my ligand away from my protein with
the same
mdp file and I obtained two different plots - Force vs
time (The
breaking point occured at different times with different
force).
Can you please explain?
If you change the stiffness of the spring, you change the
magnitude
of the applied force. Thus, the behavior you see will occur
either
faster or slower, depending on the strength of the spring.
-Justin
So how can I change the stiffness of my spring?
By changing pull_k1. I thought that's what you meant you had
already done, but I can see now that my interpretation wasn't
correct. Understand the SMD is a non-equilibrium, path-dependent
process. I don't know what you're pulling from what, but if the
interactions are slightly different along the dissociation pathway,
the forces are different because the path is different.
-Justin
I used exactly the same mdp file with the same parameters - the same
same pull_k1 as well and I obtained different plots. The starting
configuration is also the same. I pull a ligand away from the protein.
Would you obtain from two normal MD or SMD simulations with the same
starting configuration different results?
Yes, it's quite possible. MD is a chaotic process.
http://www.gromacs.org/Documentation/Terminology/Reproducibility
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation
-Justin
--
========================================
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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