[gmx-users] pulling simulations
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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