[gmx-users] Justin umbrella sampling tutorial......

Justin A. Lemkul jalemkul at vt.edu
Thu May 24 07:42:50 CEST 2012

On 5/24/12 7:40 AM, rama david wrote:
> Hi Justin,
> Thank you for your Reply
> Before start tutorial I read your paper, It help me
> a lot to understand the concept of umbrella sampling...
> But truly I not understand the part in six step
>   why to use define -DPOSRES_B  and not -DPOSRES,
> I think I miss it ...
> I will be a very greatfull to you, if you shade
> some light on these ....

Using -DPOSRES_B restrains only one chain of the protein, thus mimicking the 
stability of a larger macromolecular assembly.  Using -DPOSRES restrains all 
protein chains, which accomplishes nothing when trying to do umbrella sampling. 
  The chain to which the umbrella potential is applied would not be able to move 
at all, thus rendering the pull force measurements ineffectual.



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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