[gmx-users] a question related to NMR

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 13 14:02:44 CEST 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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