From: "Zhao Lifeng" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: <[email protected]>
Subject: [gmx-users] About calculations of viscosity
Date: Fri, 12 May 2006 18:47:53 +0800
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.
For the first NEMD method you need to use the deform option, not accelerate.
Accelerating the whole system has no effect.
I¡¯m eager for any instructions about techniques on the calculations and
the value ranges.
I think you basically understood the methods.
You should choose the values such that you still have a linear response.
For the ranges you can have a look at the literature.
It is best to try different values and check when the response becomes
non-linear.
Berk.
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