# [gmx-users] calcualting viscosity from NEMD

Qiao Baofu qiaobf at gmail.com
Thu Oct 12 13:40:16 CEST 2006

```Hi all,

I want to calculate the shear viscosity of a small molecule pure fluid.
Therefore, I run some non-equilibrate MD. But I don't know what values
should be given to "accelerate" and "cos-acceleration".

Please see my results below. I found that:
1.  with the "cos-acceleration" decreasing, 1/viscosity decrease almost
continuously, and the rmsd increase.
2.  The value of "accelerate" doesn't affect 1/viscosity greatly.
Thus "accelerate=0.1" is acceptable, but how about the "cos-acceleration"?

Who has such experience? Can you give me some suggestions? Thanks in

1. md4
#accelerate               = 0.1  0   0  -0.1   0   0
#cos-acceleration         = 0.5
Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------
2CosZ*Vel-X                0.170636  0.0329107  0.0328585 -6.414e-06  -
0.006414
1/Viscosity-(SI)            944.025    183.219    182.931 -0.0355854   -
35.5855

2. md5
#accelerate               = 0.1  0   0  -0.1   0   0
#cos-acceleration         = 0.3
Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------
2CosZ*Vel-X               0.0323069  0.0181729  0.0180577 7.07857e-06
0.00707858
1/Viscosity-(SI)            294.808    165.922    164.855  0.0650939
65.094

3. md6
#accelerate               = 0.1  0   0  -0.1   0   0
#cos-acceleration         = 0.1
Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------
2CosZ*Vel-X              0.00130712  0.0156865  0.0156829 -1.16341e-06 -
0.00116341
1/Viscosity-(SI)            35.5201    426.066    425.967 -0.0316935   -
31.6935

4. md9
#accelerate               = 0.1  0   0  -0.1   0   0
#cos-acceleration         = 0.05
Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------
2CosZ*Vel-X              0.000350432  0.0149682  0.0149682 -7.67601e-08 -
7.67602e-05
1/Viscosity-(SI)            19.0263    812.332    812.331 -0.00409487   -
4.09487

5. md10
#accelerate               = 0.1  0   0  -0.1   0   0
#cos-acceleration         = 0.01
Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------

2CosZ*Vel-X              0.000121789  0.0152012  0.0152012
0          0
1/Viscosity-(SI)            33.0229    4123.09    4123.09 -0.00116304   -
1.16304

6. md11
#accelerate               = 0.1  0   0  -0.1   0   0
#cos-acceleration         = 0.005
Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------
2CosZ*Vel-X              -4.23371e-05  0.0153689  0.0153689 1.35182e-07
0.000135182
1/Viscosity-(SI)           -22.9384    8335.83     8335.8  0.0741577
74.1578

***************************************************************************************************************
7. md7
#accelerate               = 0.3  0  0    -0.3  0  0
#cos-acceleration         = 0.1
Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------
2CosZ*Vel-X              0.00107554  0.0153412   0.015341 -2.26469e-07 -
0.000226469
1/Viscosity-(SI)            29.1877    416.411    416.407 -0.00612827   -
6.12828

8. md8
#accelerate               = 0.5  0  0    -0.5  0  0
#cos-acceleration         = 0.1
Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------
2CosZ*Vel-X               0.0011791   0.014806  0.0148055 -4.10365e-07 -
0.000410365
1/Viscosity-(SI)            32.0258    402.128    402.115 -0.0110667   -
11.0667
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