[gmx-users] pulling simulations

Justin Lemkul jalemkul at vt.edu
Thu May 30 04:22:45 CEST 2013

On 5/29/13 9:19 AM, Sathish Kumar wrote:
> Dear Sir,
>                           In pulling simulations how to set pull_rate and
> pull_k .On which basis we can set these values.

There is no systematic way to set these values, at least none that I know of. 
Everyone has their own impression of what is "right" throughout the literature. 
  The burden of proof is on you to show that your settings don't lead to 
anomalous behavior.  Pull too fast or strong and you might deform some essential 
part of your system.  Pull too slowly or weakly and you may never see the 
behavior you wish to observe.  Try a systematic analysis of different rates and 
constants to see (1) what combinations actually work and (2) which of those 
combinations are practical for the scope of what you are doing.



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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