[gmx-developers] Fw: About calculations of viscosity

David van der Spoel spoel at xray.bmc.uu.se
Thu May 18 08:48:07 CEST 2006

> I’m a new GMX user. I notice from either the user-manual or the 
> references (Palmer, PRE 49 359, & B. Hess, JCP 116, 209, etc.) that 
> there seem to be at least 3 methods available in Gromacs: Einstein 
> relation, TCAF and periodic perturbation method. But I’m not very clear 
> about how to set the calculations and how to get the according viscosity 
> values.
> My understanding is this:
> For Einstein relation calculations, there is no special setting in the 
> md.mdp file, and the viscosity value is gotten by the visco.xvg file 
> generated by ‘g_energy –vis’;
> For TCAF, also there is no special setting in the md.mdp file, and the 
> viscosity value is gotten by fitting the data of visco_k.xvg file 
> generated by ‘g_tcaf’;
> For the periodic perturbation method, two NEMD items, a ‘accelerate’ 
> value in X direction should be specified to all atoms and a 
> ‘cos_acceleration’ value should be given, and the viscosity value is 
> gotten from the ‘1/Viscosity(SI)’ item of the ‘g_energy’ results.
> I’m eager for any instructions about techniques on the calculations and 
> the value ranges.
> Thanks.

According to Hess, the periodic perturbation is more efficient than 
other methods. In particular methods that depend on the pressure 
autocorrelation tend to need very long simulation times to converge.
We have used the NMED method by Hess (JCP 119 pp. 7308-7317, 2003) as 
well and I will use it again. It is important to test different 
accelerate values, and notice that the real viscosity is obtained in the 
limit that the external perturbation goes to zero.

> Lifeng Zhao
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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