[gmx-users] on the NPT equilibration of the on-line tutorial of lysozyme

[Justin A. Lemkul]

Acoot Brett wrote:
> Dear All,
>  
> For the on-line tutorial of *Justin Lemkul on *NPT equilibriation 
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html), 
> if we extend the npt simulation time from 100 ps to 200 ps, is any 
> possibility that the black pressure curve would be smooth? Is this 
> extension necessary  in order to get the smooth black curve?
>  

No.  Pressure fluctuates wildly under normal conditions.

http://www.gromacs.org/Documentation/Terminology/Pressure

> I install my gromacs under cygwin. When I do
> DISPLAY=:0.0 xmgrace -nxy Density.xvg,
>  
> only the non-smoothed black cure exist, and the red curve does not 
> exist. Will you please tell me how to have the red curve occur?
>  

In Xmgrace, Data -> Transformations -> Running Averages.  I think the sliding 
window was 100 data points.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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