[gmx-users] US and SMD

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri May 10 07:55:02 CEST 2013


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?

Thanks in advance.
Your suggestionswould be appreciated .


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