Hi,
I "fixed" an issue with the 1/visc output in 4.5.4, but incorretly.
I filed a bug report and a fix, you can easily correct your numbers:
http://redmine.gromacs.org/issues/1244
https://gerrit.gromacs.org/#/c/2370/
Thanks for reporting this.
Cheers,
Berk
> Date: Thu, 11 Apr 2013 16:55:37
There have been several bug fixes related to viscosity calculations since the
release of version 4.5.3, of which at least one (on 1/10/2011) specifically
mentions zero viscosity in the .edr and .log files.
I would suggest pulling the latest release-4-5-patches from the git repository
and try
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: September 29, 2010 1:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation
On 2010-09-29 20.52, Payman Pirzadeh wrote:
> Well, two questions:
>
> 1. My bulk values are fluctuati
olvent (water)?
>
> Payman
>
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Justin A. Lemkul
> Sent: September 29, 2010 12:28 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users]
water)?
Why not use g_msd?
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: September 29, 2010 12:28 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation
P
list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation
Payman Pirzadeh wrote:
> Hello,
>
> I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity
> of my system which is water. Two files are generate: *.xvg and the
> enecorr.xvg. Now, what
Payman Pirzadeh wrote:
Hello,
I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity
of my system which is water. Two files are generate: *.xvg and the
enecorr.xvg. Now, what should I do to calculate the viscosity of my
system with these two files? Sorry for such naïve ques
e the k=0.
>
>Berk
>
>Date: Fri, 13 Mar 2009 07:33:30 +
> From: jesb...@rediffmail.com
>To: gmx-users@gromacs.org
>Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
>CC:
>
>
> Dear Berk and David,
>
>
>
>
i, 13 Mar 2009 07:33:30 +
From: jesb...@rediffmail.com
To: gmx-users@gromacs.org
Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
CC:
Dear Berk and David,
Thank you very much for your
appropriate and informative replie
12 Mar 2009 07:39:52 +
> From: jesb...@rediffmail.com
>To: gmx-users@gromacs.org
>Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
>CC:
>
>
>David,
>
>
>
>Thanks for the quick reply.
>
>
>
>Indeed I did as what you suggeste
Berk
Date: Thu, 12 Mar 2009 07:39:52 +
From: jesb...@rediffmail.com
To: gmx-users@gromacs.org
Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
CC:
David,
Thanks for the quick reply.
Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg
David,
Thanks for the quick reply.
Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg
The output file created includes three columns.
1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity.
It seems, the unit given is cp. ( 1cp= 1* 10¯3 Pascal Second).
The b
JMandumpal wrote:
Dear GROMACS users,
As explained in the manual ( page 139, section
6.5/3.3.3) I would like to calculate viscosity of my system ( water)
using g_energy. I opted(40 Mu-X ) from the g-energy selection. But
the unit written on the Y axis of the cor
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