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Dear gmx-users,
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. Thanks.
Zhao |
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