[gmx-users] regarding calculation on shear viscosity

[shakuntala dhurua]

---------- Forwarded message ---------
From: Madhurima Jana <tinni.217 at gmail.com>
Date: Thu, Feb 27, 2020 at 12:10 PM
Subject: Re: problem regarding calculation on shear_viscosity
To: shakuntala dhurua <madhu.dhurua94 at gmail.com>



Dear All,

I have calculated shear viscosity (from 5 ns production trajectory) of bulk
> water (900 water molecules) by using the following command.
>


> gmx tcaf -n index.ndx -s water_packmol_30a_pro5.tpr  -f
> water_packmol_30a_pro5.trr  -oc water_packmol_30a_pro5_wat_tcaf.xvg ,
>


> In the output file named visc_k.xvg , I found that while the eta values
> for different k are in the range of 0.3 to 0.5 cp,  sudden increase in eta
> value of 12 cp occurs in one case. I am unable to trace the reason behind
> it. Hence I request your help to know if I am doing anything wrong. The
> visc_k.xvg file is attached for your reference.
>

Thanks in advance,
Shakuntala