On 2013-06-02 06:40, Marcelo Vanean wrote:
*On 2013-06-01 17:11, Marcelo Vanean wrote:
*
*On 2013-06-01 02:24, Marcelo Vanean wrote:
*
*Hello to everyone. In version 4.5.5, calculating the viscosity with the
command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and
visco.xvg)
On 2013-06-01 17:11, Marcelo Vanean wrote:
On 2013-06-01 02:24, Marcelo Vanean wrote:
Hello to everyone. In version 4.5.5, calculating the viscosity with the
command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and
visco.xvg) are inconsistent. The file evisco.xvg, for example, g
On 2013-06-01 02:24, Marcelo Vanean wrote:
Hello to everyone. In version 4.5.5, calculating the viscosity with the
command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and
visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a
value of zero for viscosity using the
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
Dear Email Sender,
Thank you very much for contacting me! Unfortunately, I am not available in the
office at the moment and cannot respond to your email. I will be able to handle
your request starting again Thursday, August 4, 2011.
For all questions about CloudBroker and the CloudBroker Platfo
On Wed, 2011-06-01 at 23:37 +0200, Thomas Koller wrote:
> Hello,
>
> I calculate the viscosity with g_energy using option -vis (Gromacs
> 4.0.7):
>
> g_energy -f file.trr -s file.tpr -vis visc.xvg
>
> Why do I get viscosity values only until the half of the simulation
> time?
This results f
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
Xiaohu Li wrote:
Hi,
I'm trying to calculate viscosities of a few ionic liquid and has
roughly read about Hess's paper JCP 116 209, 2002.
Follows are the questions that I have
(1) For the method which uses the fluctuations of the pressure tensor
using Green-Kubo relation. I used g_energy
rds,
I recommend that you read the paper by Hess (JCP 2002) about viscosity.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Dallas Warren
Sent: September 29, 2010 7:11 PM
To: Discussion list for GROMACS users
Subject: RE: [
-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Dallas Warren
Sent: September 29, 2010 7:11 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] viscosity calculation_2
Sorry, haven't looked at these files before so this might not be the
case,
Sorry, haven't looked at these files before so this might not be the
case, but doesn't the top of the .xvg file explain what each column is?
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville V
: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: September 29, 2010 2:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation_2
On 2010-09-29 22.00, Payman Pirzadeh wrote:
> Adding to my previous comme
Message-
From: gmx-users-boun...@gromacs.org [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
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 fluctuating around 60 (I assume cP). But it looks
like
> very weird
[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
On 1/8/10 1:59 AM, Lum Nforbi wrote:
Dear all,
Below is my output for viscosity determination. In order to get a
value for the viscosity, do I just take an average of the numbers in the
third column?
In principle I think this is correct, but check the source code to make
sure. You may also
Vitaly V. Chaban wrote:
Hi,
When using g_energy to calculate viscosity ("g_energy -vis"), in
enecorr.xvg the ACF of stress tensor is output. How can one specify
the "acflen" of this ACF?
I try the key "g_energy -vis -acflen XXX" but the length of the ACF is
still equal to the half of the traject
Dear Berk:
Thank you so much for your help!
I read your paper: " Determing the shear viscosity of model liquids from
molecular dynamics simulations" You used NVT? My question is which one is
better? NPT or NVT?
"Strictly speaking it might be incorrect, but since pressure scaling is
usually less
Dear Herk:
Thank you so much for your help!
Maybe the way I asked make it confusing. I read your paper: " Determing the
shear viscosity of model liquids from molecular dynamics simulations" You
used NVT. My question is which one is better? NPT or NVT? Or you can use
either of them.
"Strictly sp
Hi,
Yes, you can use NPT, the code takes care of this properly.
Strictly speaking it might be incorrect, but since pressure scaling is usually
less than 1%
it will not affect your results significantly.
Berk.
Date: Mon, 25 May 2009 15:19:10 -0700
From: yson...@asu.edu
To: gmx-users@gromacs.org
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
From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Viscosity in PE
Date: Thu, 07 Sep 2006 19:36:34 +0200
Esther Caballero-Manrique wrote:
You can calculate it from the ve
] Viscosity in PE
>From: David van der Spoel <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: Discussion list for GROMACS users
>Subject: Re: [gmx-users] Viscosity in PE
>Date: Thu, 07 Sep 2006 19:36:34 +0200
>
>Esther Caballero-Manrique wrote:
>
From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Viscosity in PE
Date: Thu, 07 Sep 2006 19:36:34 +0200
Esther Caballero-Manrique wrote:
You can calculate it from the ve
Esther Caballero-Manrique wrote:
You can calculate it from the velocity autocorrelation function, which
can be calculated using the g_velacc. The friction can be calculated
from the integral of the velocity autocorrelation function
(friction=3KbT/(integral of vacf)) and then the viscosity can b
You can calculate it from the velocity autocorrelation function, which
can be calculated using the g_velacc. The friction can be calculated
from the integral of the velocity autocorrelation function
(friction=3KbT/(integral of vacf)) and then the viscosity can be
calculated using Stoke's equati
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