Den 2018-04-06 kl. 01:55, skrev Ali Ahmed:
Hello David,
I have the same problem
I run the simulation for 10 ns and I saved energies every 1 ps but the
results were far and the curves go to negative values.
Please, do have an idea how to get accurate results?
Thank you
Ali


You give no information on numbers or what the einstein viscosity curve look like.




On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel <sp...@xray.bmc.uu.se>
wrote:

Den 2018-04-05 kl. 09:19, skrev Jo:

Hello,

I would like to calculate bulk and shear viscosity on gromacs using
g_energy.  I have read a number of other emails about this topic but there
still seems to be no conclusive answer to how to use this tool.  I use the
following command:

gmx energy -f  prod_500.edr -vis viscosity.xvg


The einstein viscosity is usually more accurate. How long is your
simulation and how often do you save the energies?


 From this, a file called 'viscosity.xvg' is produced with data on time

(ps), shear viscosity, and bulk viscosity.  However, these values
fluctuate
wildly and are off from the correct viscosity for this model (SPCE) by at
least an order of magnitude.  I know the simulation trajectory is correct
as I have matched potential energy, density, and diffusion coefficition
for
these runs with literature.  However, the viscosity numbers are far off
from the expected values.

Any suggesions on what I can try?  I assume there must be a way to do it
by
hand via the pressure tensors.  Can someone directly me to how I can
practically take the pressure tensors to calculate via Green-Kubo method
the viscosity?

Thanks,

Shuwen



--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

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--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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