Acoot Brett wrote:
Dear All,
Before we run the production MD, we have minimized the energy and
equilibriated the system. Especially we will keep the temperature
constant. Then which force drive the protein to converge? Why the
protein do not reverse its already completed MD process before it
converges, leading to that the system will never converge? Which
computation technique is adopted so that the production MD will be in
the process of converging?
Do not assume that a converged simulation necessarily produces one "correct"
structure. A converged simulation will still move over time, but the ensemble
of structures that it samples does not change. For instance, you'll never get a
protein to stay put. It will wiggle around within a defined set of
configurations that define its stability and inherent dynamics. The time over
which this takes to occur depends on a lot of factors and cannot be easily
generalized. There is no special technique to force a simulation to converge,
you just have to wait.
-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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