[gmx-users] shear viscosity

[Ahmet yıldırım]

Dear users,

g_energy -f *.edr -vis

I have two questions about the results of eviscoi.xvg ( derivative of
Einstein relation):

1.) I dont understand the unit of y-axis. It is kg.m^(-1).s^(-1).10^(-3) in
B.Hess 2002

In eviscoi.xvg
@yaxis  label (kg m\S-1\N s\S-1\N ps)
That is
The unit of y-axis:kg.m^(-1).s^(-1).ps

What is that?
kg.m^(-1).s^(-1).ps equals to kg.m^(-1).s^(-1).10^(-3)?

2.) There are 5 columns in eviscoi.xvg. 1th is time. What are the rest?


By the way, there is 216 water molecules in spc216.gro. But I want to
calculate the shear viscosity of 512 water molecules. How can I get/derive
512 water molecules from spc216.gro? Can anyone give me some hint of this?

Thanks in advance

-- 
Ahmet Yıldırım
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[gmx-users] Shear viscosity

[Vitaly V. Chaban]

Hi all,

I am trying to master the art of shear viscosity calculation using
g_energy -vis. Plotting the first column in visco.xvg over time, the
nearly straight line is obtained. Is it OK? How can one get the
viscosity value from these data? My simulation details for this task
are: NVT, 298K, shifted LJ with a big Rcut, PME, the substance is an
ionic liquid, simulation time is 2 ns with 1 fs timestep and every
10fs saving to ener.edr.

I suspect something is definitely wrong in my calculation of
viscosity. I tried the same procedure with SPC water (NPT, 1ns, PME,
shifted LJ) and got the complicated curve (in visco.xvg, first column)
with an average value of 0.55 cP. This result seems to be quite more
realistic as for me. Then what is the possible source of problem in my
above setup?

Thanks for any suggestions.
Vitaly
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