[gmx-users] viscosity calculation using g_energy
aa5635737 at gmail.com
Sun Apr 8 09:10:03 CEST 2018
On Thu, Apr 5, 2018 at 6:55 PM, Ali Ahmed <aa5635737 at gmail.com> wrote:
> 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
> On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel <spoel at xray.bmc.uu.se>
>> Den 2018-04-05 kl. 09:19, skrev Jo:
>>> 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
>>> still seems to be no conclusive answer to how to use this tool. I use
>>> 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
>>> 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
>>> 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
>>> 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?
>> 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.
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