[gmx-users] a question related to NMR

[Justin A. Lemkul]

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

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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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