[gmx-users] Umbrella_pull_simulation

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 24 15:26:48 CET 2012

shahid nayeem wrote:
> I thought this time to be sufficient without any reasonable basis.

If you pick an arbitrary time frame, you're going to get results with arbitrary 
accuracy.  Your time frame should be decided based on a whole host of factors, 
not the least of which include an assessment of the types of interactions in the 
system and how they may decay as a function of distance, as well as the 
individual convergence of observables in each simulation.  This is true of any 
simulation.  Only after you can conclude that each window has converged can you 
expect to draw any reasonable conclusions.



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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