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 evi
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
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 Einstein relation. Another question
in 4.0.7,
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
Dear gmx-users,
I have posted this question on gmx-users list few days ago 2-3 times.
But I didn't receive any suggestion/reply.
I have searched a lot on previous posts related to Viscosity calculations
but unable to
get any suitable reply.
Please reply if someone has solution of following problem
Dear gmx-users,
I am trying to learn viscosity calculations using non-equilibrium
method in Gromacs 4.5.4. I have gone through Hess paper and several
posts on viscosity calculation.
I have setup a system of pure water (32000 molecules) and run till 10 ns
using NPT and setting
cos-acceleration=0.1
Dear Gromacs Users,
I am trying to learn viscosity calculations using non-equilibrium
method in Gromacs 4.5.4. I have gone through Hess paper and several
posts on viscosity calculation.
I have setup a system of pure water (32000 molecules) and run till 10 ns
using NPT and setting
cos-acceleration=
Dear Email Sender,
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Dear Gromacs Users,
I am trying to learn viscosity calculations using non-equilibrium method in
Gromacs 4.5.4. I have gone through Hess paper and several posts on viscosity
calculation.
I have setup a system of pure water (32000 molecules) and run till 10ns using
NPT and setting
cos-accelerati
Sir,
I am dealing with MD simulation of ionic-liquids.I want to calculate viscosity
of this system.I am trying to do it by using Green-Kubo relation for the
transport properties; it is time integral of pressure correlation function but
I am stuck with how to get the pressure correlation funct
Dear gmx-users,
I am trying to simulate coarse-grained dodecane using MARTINI force field. One
of the properties I would like to measure is viscosity. I was trying to do this
from NEMD (actually I am using Langevin stochastic dynamics) and I am facing
the problem having negative(!) value for
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
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?
Thomas
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman
Hello,
I want to calculate bulk viscosity and surface tension. Gromacs 4.0.7 provides
options in g_energy:
1) Do I need long simulations to get a constant value for the bulk viscosity
using -vis option?
2) How is the surface tension (#Surf*SurfTen) calculated?
Regards,
Thomas
--
Empfehlen S
Sir,
I request you to discuss the way to find out some properties like
viscosity, heat of vaporisation , spatial heterogeneity using Gromacs-4.5.3
from the obtained production run trajectories data for any liquid(I am dealing
with Ionic liquids) .The Gromacs utility has option for sur
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
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
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 -f *.edr -s *.tpr -vis o
Hello,
I am trying to calculate the viscosity of my pure water system at 275K. The
system has run for 40ns. I issued the following command:
g_energy_d_mpi -f 275K_50_50_50_2.edr -s 275K_50_50_50_2.tpr -nmol 4202 -vis
sixsitewater_275K -b 0 -e 4
The numbers I get in the output file are
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
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
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
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?
# This file was created Wed Jan 6 16:25:24 2010
# by the following command:
# g_energy -f wfullmdrun_ener.edr -vis viscosity.xvg
#
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
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 trajectory length.
Thanks,
Vital
> 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@
May 2009 15:19:10 -0700
> From: yson...@asu.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Viscosity using periodic perturbation method
>
>
> Dear users:
>
> I was trying to calculate the viscosity of liquid system using periodic
> perturbation method. Does thi
@gromacs.org
Subject: [gmx-users] Viscosity using periodic perturbation method
Dear users:
I was trying to calculate the viscosity of liquid system using periodic
perturbation method. Does this method require NVT ensemble simulation in stead
of NPT ? Because I read some literature on periodic perturbation
Dear users:
I was trying to calculate the viscosity of liquid system using periodic
perturbation method. Does this method require NVT ensemble simulation in
stead of NPT ? Because I read some literature on periodic perturbation
method. they all used NVT. I did not found any information about this
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
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
Title: Viscosity in PE
Dear Gromacs-users
I have already run some MD, both in NVT and NPT, of Polyethylene (1000 atoms-backbone).
I would like to estimate the viscosity of my systems. Is it possible even if it is a rubbery solid? Which method is the most suitable?
Regards
Alessandro Mattoz
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