[gmx-users] About calculations of viscosity
zhaolf at sjtu.edu.cn
Fri May 12 12:47:53 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 ¨Cvis¡¯;
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.
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