[gmx-developers] Fw: About calculations of viscosity

[Zhao Lifeng]

----- Original Message ----- 
From: Zhao Lifeng 
To: gmx-users at gromacs.org 
Sent: Friday, May 12, 2006 6:47 PM
Subject: About calculations of viscosity


Dear gmx-users,

I'm sorry to send the mail abruptly. I had emailed this message to gmx-users at gromacs.org days before, but there was no reply. Thank you very much for your kindly reading this email and I expect your as kind instructions.

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.



Lifeng Zhao
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