# [gmx-users] viscosity

leona taba taba_leona at yahoo.com
Fri Sep 16 13:01:39 CEST 2005

``` i wanna know the viscosity of the water molecules in
the protein in water and elasticity of protein also. I
used g_energy -vis , the result looked like the
following. I searched literature of viscosity and
elasticity, however it is still hard to understand the
values i get from gromacs. I'd like to know the site
that describe how to calculate viscosity more simple
than i searched. how to calculate elasticity also.
the following is what i get from gromacs.
1.
@    title "Bulk Viscosity"
@    xaxis  label "Time (ps)"
@    yaxis  label "\8h\4 (cp)"
@ s0 legend "Shear"
@ s1 legend "Bulk"
19.6078     141.175     73.7458
39.2157     155.547     47.1863
58.8235      179.24     45.0737
78.4314      188.36     39.2445
98.0392     199.355     30.7009
2.
@    title "Shear viscosity using Einstein relation"
@    xaxis  label "Time (ps)"
@    yaxis  label "(kg m\S-1\N s\S-1\N)"
@TYPE xy
10  0.00162696  0.00143204  0.00113582
0.00139827
30  0.00184312  0.00160504  0.00134872
0.00159896
50  0.00154051  0.00212251  0.000928209
0.00153041
70  0.00151729  0.00170263  0.000904012
0.00137464
90  0.00172047  0.00149091  0.000669996
0.00129379
3.
@    title "Shear viscosity integral"
@    xaxis  label "Time (ps)"
@    yaxis  label "(kg m\S-1\N s\S-1\N ps)"
@TYPE xy
20   0.0325392   0.0286408   0.0227164
0.0279655
40   0.0694017   0.0607415   0.0496908
0.0599447
60    0.100212    0.103192    0.068255
0.0905529
80    0.130558    0.137244   0.0863352
0.118046
> what is the number of  vicosity and  that value is
calculated from water molecules only?
leona taba

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