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