2013 16:55:37 +0900
> From: jamesresearch...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Viscosity calculation using cos_acceleration
>
> Dear Gromacs users,
>
> This question seems to come up periodically in the mailing list, but none
> of the pre
Dear Gromacs users,
This question seems to come up periodically in the mailing list, but none
of the previous answers seem helpful in my case.
I'm trying to reproduce the viscosity calculation of SPC water by Berk Hess
(JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get is 2
order
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
Hi, all,
I was trying to reproduce the viscosity results of SPC water reported in
Berk Hess' paper (JCP, vol.116 No.1, 209-217, 2002) by using the
periodic perturbation method. After reading some old tips on the
maillist exchanged by Song, David, etc., I tried to set up the NVT
simulation jus
[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
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 question.
Regards,
Payman
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
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 corresponding xvg file
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