Hello,
I am trying to calculate the viscosity of pure SPCE water, which has a bulk
viscosity of 1.567 cP and shear viscosity of 0.704 cP according to
literature (https://pubs.acs.org/doi/pdf/10.1021/jp211952y).
In gromacs, I ran 1000 SPCE water using NPT equilibration for 20 ns and
then NVE
Den 2018-04-08 kl. 17:31, skrev Ali Ahmed:
Hello David,
Thank you for your reply,
After 5 ns of equilibrium, I run the simulation for 10 ns of heptane, but
in the results of Einstein viscosity, I got only 5 ns.
There are two files evisco.xvg and viscosity .xvg. In the first one, there
are
Hello David,
Thank you for your reply,
After 5 ns of equilibrium, I run the simulation for 10 ns of heptane, but
in the results of Einstein viscosity, I got only 5 ns.
There are two files evisco.xvg and viscosity .xvg. In the first one, there
are different columns but I think the last one is the
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
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
On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel
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
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
Hello,
I would like to calculate viscosity of a box of water using g_energy. I
used the line g_energy -f production.edr -vis viscosity.xvg, where the
viscosity.xvg generated shows bulk and shear viscosity (cP) by time (ps).
However, the value are several orders of magnitude above the correct
