[gmx-users] Justin's Paper

[Justin A. Lemkul]

On 6/28/12 7:12 AM, Steven Neumann wrote:
> Hey Justin,
>
> J. Phys. Chem. B, 2010, 114 (4), pp 1652–1660
> DOI: 10.1021/jp9110794
> Publication Date (Web): January 7, 2010
>
> I am wondering whether you calculated the free energy from windows
> obtained using different pulling rates (0.01, 0.005,. 0.001 nm/ps) ?

These are the values used during SMD, not umbrella sampling (which uses a zero 
pull rate).  The different pull rates were applied to show that there was no 
bias on the resulting configurations generated.

> Do you think you would get the same deltaG value?
>

The configurations generated were nearly identical, so the starting points for 
the umbrella sampling would have been quite similar, as a result.  I see no 
reason to think that this pull rate is associated with the outcome of umbrella 
sampling.  Adequate simulation time should give sufficient sampling and a 
reliable value of DeltaG.

-Justin

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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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