[gmx-users] RE:Shear viscosity/bulk viscosity

[Junfang.Zhang at csiro.au]

Dear Mark,

Thank you very much for your prompt reply.

visco.xvg looks like

# This file was created Wed Jun 20 10:49:51 2007
# by the following command:
# g_energy_d -vis -f run2.edr 
#
# g_energy_d is part of G R O M A C S:
#
# Great Red Oystrich Makes All Chemists Sane
#
@    title "Bulk Viscosity"
@    xaxis  label "Time (ps)"
@    yaxis  label "\8h\4 (cp)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Shear"
@ s1 legend "Bulk"
    1.9998     9.73437     9.46535
    3.9996     9.81396     9.30671
    5.9994     9.80349     9.06717
	.
	.
	.
evisco.xvg:

# This file was created Wed Jun 20 10:49:51 2007
# by the following command:
# g_energy_d -vis -f run2.edr 
#
# g_energy_d is part of G R O M A C S:
#
# Great Red Oystrich Makes All Chemists Sane
#
@    title "Shear viscosity using Einstein relation"
@    xaxis  label "Time (ps)"
@    yaxis  label "(kg m\S-1\N s\S-1\N)"
@TYPE xy
         1  0.000717139  0.000709325  0.000707105  0.00071119
         3  0.00103297  0.00101052   0.0010127  0.00101873
         5  0.00104859  0.00104779  0.00108397  0.00106012
         7  0.00106196  0.00106595  0.00109727  0.00107506
         9  0.00107086  0.00106848  0.00109889  0.00107941
        11  0.00107609  0.00107371  0.00110653  0.00108544
		.
		.
		.

Regards and thanks,

Junfang






-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Thursday, 21 June 2007 12:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] RE:Shear viscosity/bulk viscosity

Junfang.Zhang at csiro.au wrote:
> Dear Gromacs Users,
> 
> 
> When I use the command
> 
> g_energy_d  -vis -f  *.edr 
>  
> files such as, evisco.xvg and visco.xvg are generated. evisco.xvg have
4
> columns and viso.xvg has 2 colums. Can you please let me know what
they
> are, as I failed to find the explanations in 6.5 of the manual and the
> paper published in the Journal of chemical physics 116:209-217, 2002. 

Thanks for letting us know how you've tried to solve the problem. Do the

comments on the top of the .xvg file clarify this?

Mark
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