[gmx-users] calcualting viscosity from NEMD

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 12 14:10:44 CEST 2006

Qiao Baofu wrote:
> 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 
> advances!
you should only use cos_accelerate and try different small values 
between 0 and 0.5
then frm there extrapolate to zero
accelerate is for other stuff.

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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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