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
--
========================================
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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