[gmx-users] US and SMD

Justin Lemkul jalemkul at vt.edu
Fri May 10 11:59:44 CEST 2013

On 5/10/13 1:55 AM, Shima Arasteh wrote:
> Hi,
> In Umbrella Sampling method, among mdp settings, there is a section where the pull code settings are defined in:
> pull = umbrella: using a harmonic potential to pull
> As it is said that "with US the path of the permeating ion along thereaction coordinate is sampled using many discrete windows, whereas with SMD the ion is pulledalong this same reaction coordinate",
> I am on a doubt that how the pull code with a harmonic potential works here? I am little confused.
> Would you please giveme a hint to understand it?

To carry out umbrella sampling with the pull code, you restrain configurations 
at varying distances with a harmonic potential (see my tutorial for an example, 
and the vast body of literature on this topic for the underlying theory).  SMD 
can be conducted in a number of ways and need not involve a harmonic potential. 
  The two techniques (US and SMD) are different, but make use of common portions 
of code since some aspects are somewhat similar.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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