[gmx-users] About calculations of viscosity

[Berk Hess]

>From: "Zhao Lifeng" <zhaolf at sjtu.edu.cn>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>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.