[gmx-users] US and SMD

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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