Re: [gmx-users] viscosity

[David van der Spoel]

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) 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, the file eviscoi.xvg is approximately a straight line, whereas
in
version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way?
Evidently, there is an inconsistency in these different results. Help me,
please.


*


*I used the same energy file (ener.edr) and I get this results:
http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals.

*


*Maybe you can post the energy file on that site as well.

Have you tried to compute the pressure autocorrelation (using g_energy)?*

I didn't the pressure autocorrelation. A question: what does this analysis
tell me?
Check the equations in the manual and relevant literature. The viscosity 
is computed from the pressure ACF.



I posted the energy file here:
http://www.4shared.com/file/SSAU1reN/ener.html.


That website does not work.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] viscosity

[Marcelo Vanean]

*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, gives a
>> value of zero for viscosity using the Einstein relation. Another question
>> in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas
>> in
>> version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way?
>> Evidently, there is an inconsistency in these different results. Help me,
>> please.
>>
>>
>> *
>
> *I used the same energy file (ener.edr) and I get this results:
> http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals.
>
> *

*Maybe you can post the energy file on that site as well.

Have you tried to compute the pressure autocorrelation (using g_energy)?*

I didn't the pressure autocorrelation. A question: what does this analysis
tell me?
I posted the energy file here:
http://www.4shared.com/file/SSAU1reN/ener.html.
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Re: [gmx-users] viscosity

[David van der Spoel]

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, gives a
value of zero for viscosity using the Einstein relation. Another question
in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in
version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way?
Evidently, there is an inconsistency in these different results. Help me,
please.



I used the same energy file (ener.edr) and I get this results:
http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals.


Maybe you can post the energy file on that site as well.

Have you tried to compute the pressure autocorrelation (using g_energy)?

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Viscosity

[David van der Spoel]

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 Einstein relation. Another question
in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in
version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way?
Evidently, there is an inconsistency in these different results. Help me,
please.

Please give some details about your system and how you did the analysis. 
Did you use the same energy file with the different gromacs versions? In 
that case they should give the same result.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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[gmx-users] Viscosity

[Marcelo Vanean]

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, the file eviscoi.xvg is approximately a straight line, whereas in
version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way?
Evidently, there is an inconsistency in these different results. Help me,
please.
-- 
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RE: [gmx-users] Viscosity calculation using cos_acceleration

[Berk Hess]

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 +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 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
> orders of magnitude out.
> 
> My topology file and parameter file is appended at the bottom of this email.
> 
> I run g_energy and get
> 
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> 1/Viscosity 23.4689   0.132.39126  -0.255371  (m
> s/kg)
> 
> which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s
> 
> The value quoted in the paper is about 0.4 mPa.s which is around the
> correct value for water, give or take a bit.
> 
> So my question is, where is my missing factor of 100?
> 
> Any advice is much appreciated.
> 
> Thank you.
> 
> James
> 
> --
> Topology file:
> #include "ffgmx.itp"
> #include "spc.itp"
> 
> [ system ]
> Pure Water
> 
> [ molecules ]
> SOL 3456
> 
> --
> Parameter file for system (3456 SPC water molecules, 3.75x3.75x7.5 nm3 box):
> 
> ;Generic mdp file for SPC water equilibration
> ;Gromacs 4.3.x
> ;
> ;T = 300 K
> ;
> ;NVT 1.2 ns
> ;
> 
> define   =  ; define here posres etc., e.g. -DPOSRES
> 
> integrator  = md
> tinit   = 0
> dt  = 0.001
> nsteps  = 120
> 
> ; Bond constraints
> continuation = no ; switch to 'yes' if need to read in velocities etc.
> constraints =  none; constrain all bond lengths
> constraint_algorithm=  lincs   ; default
> lincs_order =  4   ; default
> 
> nstxout = 1000
> nstvout = 1000
> nstfout = 0
> nstlog  = 1000
> nstenergy   = 1000
> ; Output frequency and precision for xtc file
> nstxtcout   = 1000
> xtc-precision   = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps=
> ; Selection of energy groups
> energygrps  = System
> 
> ; Neighbor list
> ns_type  =  grid; neighlist type
> nstlist  =  5   ; Freq. to update neighbour list
> rlist=  0.9 ; nm (cutoff for short-range NL)
> pbc = xyz
> periodic_molecules   =  no
> 
> ; Non-equilibrium MD
> ;acc_grps = SYSTEM
> cos_acceleration = 0.025 ; PPM option for viscosity calculation (nm/ps²)
> coulombtype  = PME
> rcoulomb = 0.9
> optimize_fft = yes ; affects only PME calculations
> ; if you use PME, set also rcoulomb = rlist
> ; van der Waals interactions
> vdwtype  =  Cut-off; Van der Waals interactions
> rvdw =  0.9; nm (LJ cut-off)
> DispCorr = EnerPres ; long-range dispersion correction to energy and
> pressure
> 
> Tcoupl  = berendsen
> tc-grps = System
> tau_t   = 2.5
> ref_t   = 300.0
> 
> ;Pressure coupling
> Pcoupl = no
> gen_vel = no
> -- 
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[gmx-users] Viscosity calculation using cos_acceleration

[James Cannon]

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
orders of magnitude out.

My topology file and parameter file is appended at the bottom of this email.

I run g_energy and get

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
1/Viscosity 23.4689   0.132.39126  -0.255371  (m
s/kg)

which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s

The value quoted in the paper is about 0.4 mPa.s which is around the
correct value for water, give or take a bit.

So my question is, where is my missing factor of 100?

Any advice is much appreciated.

Thank you.

James

--
Topology file:
#include "ffgmx.itp"
#include "spc.itp"

[ system ]
Pure Water

[ molecules ]
SOL 3456

--
Parameter file for system (3456 SPC water molecules, 3.75x3.75x7.5 nm3 box):

;Generic mdp file for SPC water equilibration
;Gromacs 4.3.x
;
;T = 300 K
;
;NVT 1.2 ns
;

define   =  ; define here posres etc., e.g. -DPOSRES

integrator  = md
tinit   = 0
dt  = 0.001
nsteps  = 120

; Bond constraints
continuation = no ; switch to 'yes' if need to read in velocities etc.
constraints =  none; constrain all bond lengths
constraint_algorithm=  lincs   ; default
lincs_order =  4   ; default

nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog  = 1000
nstenergy   = 1000
; Output frequency and precision for xtc file
nstxtcout   = 1000
xtc-precision   = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps=
; Selection of energy groups
energygrps  = System

; Neighbor list
ns_type  =  grid; neighlist type
nstlist  =  5   ; Freq. to update neighbour list
rlist=  0.9 ; nm (cutoff for short-range NL)
pbc = xyz
periodic_molecules   =  no

; Non-equilibrium MD
;acc_grps = SYSTEM
cos_acceleration = 0.025 ; PPM option for viscosity calculation (nm/ps²)
coulombtype  = PME
rcoulomb = 0.9
optimize_fft = yes ; affects only PME calculations
; if you use PME, set also rcoulomb = rlist
; van der Waals interactions
vdwtype  =  Cut-off; Van der Waals interactions
rvdw =  0.9; nm (LJ cut-off)
DispCorr = EnerPres ; long-range dispersion correction to energy and
pressure

Tcoupl  = berendsen
tc-grps = System
tau_t   = 2.5
ref_t   = 300.0

;Pressure coupling
Pcoupl = no
gen_vel = no
--
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[gmx-users] Viscosity units: Please Reply

[Rini Gupta]

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.

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 nm/ps^2 in .mdp file.

Then, I have used following command to get viscosity from energy file.
g_energy_d -f .edr -s .tpr -o energy.xvg

and selected 1/viscosity from one of the options and I get,

Energy Average Err.Est. RMSD Tot-Drift
---

1/Viscosity 1.64374 0.0016 0.0341615 0.00789197 (m s/kg)

This gives Viscosity=1/1.64374= 0.6083 kg/ms=608.3 cP

I have some doubts regarding this result:

1) Can anyone please tell me what are the units of viscosity here.
It shows from screen output (as well from energy.xvg) that 1/viscosity
is in m-s/kg units. But, the experimental value for pure water is 0.854
cP =0.000854 kg/m-s.
So, I have a doubt regarding units coming from GROMACS it is in cP or
kg/m-s as printed. If kg/ms are the units then, this value of viscosity
for pure water is not correct ?
Please tell me what I am doing wrong here.

2) Is this a right way of calculating viscosity using NEMD or I should
do it by using 2CosZ*Vel-X option. Please tell me how can I get
viscosity from this term.

Any suggestions/comments are most welcome.

Thanks and Regards,
Dr. Rini Gupta
UBC, Vancouver
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[gmx-users] Viscosity units

[Rini Gupta]

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 nm/ps^2 in .mdp file.

Then, I have used following command to get viscosity from energy file.
g_energy_d -f .edr -s .tpr -o energy.xvg

and selected 1/viscosity from one of the options and I get,

Energy Average Err.Est. RMSD Tot-Drift
---

1/Viscosity 1.64374 0.0016 0.0341615 0.00789197 (m s/kg)

This gives Viscosity=1/1.64374= 0.6083 kg/ms=608.3 cP

I have some doubts regarding this result:

1) Can anyone please tell me what are the units of viscosity here.
It shows from screen output (as well from energy.xvg) that 1/viscosity
is in m-s/kg units. But, the experimental value for pure water is 0.854
cP =0.000854 kg/m-s.
So, I have a doubt regarding units coming from GROMACS it is in cP or
kg/m-s as printed. If kg/ms are the units then, this value of viscosity
for pure water is not correct ?
Please tell me what I am doing wrong here.

2) Is this a right way of calculating viscosity using NEMD or I should
do it by using 2CosZ*Vel-X option. Please tell me how can I get
viscosity from this term.

Any suggestions/comments are most welcome.

Thanks and Regards,
Dr. Rini Gupta
UBC, Vancouver
-- 
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[gmx-users] Viscosity calculations

[Rini Gupta]

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=0.1 nm/ps^2 in .mdp file.

Then, I have used following command to get viscosity from energy file.
g_energy_d -f .edr -s .tpr -o energy.xvg

and selected 1/viscosity from one of the options and I get,

Energy Average Err.Est. RMSD Tot-Drift
---

1/Viscosity 1.64374 0.0016 0.0341615 0.00789197 (m s/kg)

This gives Viscosity=1/1.64374= 0.6083 kg/ms=608.3 cP

I have some doubts regarding this result:

1) Can anyone please tell me what are the units of viscosity here.
It shows from screen output (as well from energy.xvg) that 1/viscosity
is in m-s/kg units. But, the experimental value for pure water is 0.854
cP =0.000854 kg/m-s.
So, I have a doubt regarding units coming from GROMACS it is in cP or
kg/m-s as printed. If kg/ms are the units then, this value of viscosity
for pure water is not correct ?
Please tell me what I am doing wrong here.

2) Is this a right way of calculating viscosity using NEMD or I should
do it by using 2CosZ*Vel-X option. Please tell me how can I get
viscosity from this term.



Thanks and Regards,
Dr. Rini Gupta
UBC, Vancouver
-- 
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Re: [gmx-users] Viscosity units

[wibke . sudholt]

Dear Email Sender,

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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 Platform, please 
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[gmx-users] Viscosity units

[Rini Gupta]

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-acceleration=0.1 nm/ps^2 in .mdp file.

Then, I have used following command to get viscosity from energy file.
g_energy_d -f .edr -s .tpr -o energy.xvg

and selected 1/viscosity from one of the options and I get,

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
1/Viscosity 1.64374 0.0016  0.0341615 0.00789197  (m s/kg)

This gives Viscosity=1/1.64374= 0.6083 kg/ms=608.3 cP

I have some doubts regarding this result:

1) Can anyone please tell me what are the units of viscosity here.
It shows from screen output (as well from energy.xvg) that 1/viscosity is in 
m-s/kg units. But, the experimental value for pure water is 0.854 cP =0.000854 
kg/m-s. 
So, I have a doubt regarding units coming from GROMACS it is in cP or kg/ms as 
printed. If kg/ms are the units then, this value of viscosity for pure water is 
not correct ? 
Please tell me what I am doing wrong here.

2) Is this a right way of calculating viscosity using NEMD or I should
do it by using 2CosZ*Vel-X option. Please tell me how can I get viscosity from 
this term.  



Thanks and Regards,
Dr. Rini Gupta
UBC, Vancouver-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] viscosity

[Prema Awati]

  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 function using Gromacs.

   Thanks.

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[gmx-users] Viscosity measurements

[Mikhail Stukan]

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 1/eta  calculated by g_energy.
Am I missing something very obvious?

I am using 4.5.4 version.

Thank you very much in advance.


My .mpd file looks like:

integrator   = sd
dt   = 0.005
nsteps = 100
comm_mode= Linear
nstcomm = 100
nstxout= 1  ; write coords
nstvout   = 1  ; write velocities
nstfout= 0   ; write forces (Do not write them)
nstxtcout= 0   ; write coords to xtc-trajectory file
nstlog   = 2000; print to logfile
nstenergy   = 100; print energies
xtc_precision  = 1000
xtc-grps  =
energygrps   = DEC

coulombtype  = Shift
rcoulomb_switch   = 0.0
rcoulomb= 1.2
epsilon_r   = 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw   = 1.2
DispCorr  = No

tc-grps  =   DEC
tau_t=   2.0
ref_t=   300

cos_acceleration =  0.1

Pcoupl   = no

gen_vel  = no
gen_temp = 300
gen_seed = 473529



=
Dr Mikhail Stukan
Schlumberger Dhahran Carbonate Research Center,
Dhahran Techno Valley  - KFUPM,
P.O. Box 39011, Dammam / Doha Camp  31942,
Kingdom of Saudi Arabia
Tel: +966 3 331 6182
Fax:+966 3 330 0845
mstu...@slb.com

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Re: [gmx-users] viscosity

[Dommert Florian]

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 from the method an autocorrelation function is averaged.
For an average that is unbiased you need the same number of samples for
every time step. You achieve this by shifting the choice of the value
for t=0 through the trajectory. The maximal length of the average you
can achieve with this is exactly half the simulation time.

/Flo
   
>  
> Thomas
>  
>  
> -- 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658


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[gmx-users] viscosity

[Thomas Koller]

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

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[gmx-users] Viscosity and surface tension

[Thomas Koller]

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

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[gmx-users] viscosity

[Prema Awati]

 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 surface tension by 
using g_energy_ d will it be proper using this option ?

 

thanks.

 project student .

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Re: [gmx-users] Viscosity calculation problems (periodic perturbation method)

[Justin A. Lemkul]

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 again.


-Justin

Xiang Gu wrote:

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 just according to Hess has done, and sent it to calculation.


Probably because not everything is properly understood, I processed the 
edr file with g_energy_d but found both the columns 2CosZ*Vel-X & 
1/Viscosity always zero. I played with several options of Tcoupl and 
tau_t, still the same happened. Could anybody experienced in this tutor 
me what has been improperly specified in the mdp file (see below; system 
is 3456 SPC water molecules contained in a 3.75*3.75*7.5 nm^3 box--just 
as in Hess' paper Table II, already well equilibrated at 300 K in 
advance; perhaps it is unnecessary to run this double precisely, but I 
was using double precision version (4.5.3.d) just because I forgot to 
switch to the single precision one, however this shouldn't cause the 
problem I had ...)?


Thanks and wish to see your suggestions soon!

Xiang Gu

;Generic mdp file for SPC water equilibration
;Gromacs 4.3.x
;
;T = 300 K
;
;NVT equilibration run, 1.2 ns
;

define   =  ; define here posres etc., e.g. 
-DPOSRES


integrator  = md
tinit   = 0
dt  = 0.001
nsteps  = 120

; Bond constraints
continuation=  no  ; switch to 'yes' if need to read 
in velocities etc.

constraints =  none; constrain all bond lengths
constraint_algorithm=  lincs   ; default
lincs_order =  4   ; default

; X/V/F/E outputs  change these according to your system 
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog  = 1000
nstenergy   = 1000
; Output frequency and precision for xtc file
nstxtcout   = 1000
xtc-precision   = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps=
; Selection of energy groups
energygrps  = System

; Neighbor list
ns_type  =  grid; neighlist type
nstlist  =  5   ; Freq. to update neighbour list
rlist=  0.9 ; nm (cutoff for short-range NL)
pbc  =  xyz ; xyz(default), no, full(infinite 
systems)

periodic_molecules   =  no

; Non-equilibrium MD
;acc_grps = SYSTEM
cos_acceleration =  0.025   ; PPM option for viscosity 
calculation (nm/ps²)


coulombtype  = PME
rcoulomb = 0.9
optimize_fft = yes ; affects only PME calculations
  ; if you use PME, set also 
rcoulomb = rlist


; van der Waals interactions
vdwtype  =  Cut-off; Van der Waals interactions
rvdw =  0.9; nm (LJ cut-off)
DispCorr =  EnerPres   ; long-range dispersion 
correction to energy and pressure


Tcoupl  = berendsen
tc-grps = System
tau_t   = 2.5
ref_t   = 300.0

;Pressure coupling
Pcoupl  =  no  ; berendsen, tau_p = 1.0 for 
faster equilibration
;Pcoupltype  =  isotropic   ; semi-isotropic: xy and z 
separately (CNT)

;tau_p   =  1.0 ; ps
;compressibility =  4.5e-5  ; 1/bar (water @ 1 atm, 300 K)
;ref_p   =  1.0 ; bar0  4000 1.034798 0.001949

gen_vel = no
;gen_temp= 300.0
;gen_seed= 173529



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Viscosity calculation problems (periodic perturbation method)

[Xiang Gu]

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 just according to Hess has done, and sent it to calculation.


Probably because not everything is properly understood, I processed the 
edr file with g_energy_d but found both the columns 2CosZ*Vel-X & 
1/Viscosity always zero. I played with several options of Tcoupl and 
tau_t, still the same happened. Could anybody experienced in this tutor 
me what has been improperly specified in the mdp file (see below; system 
is 3456 SPC water molecules contained in a 3.75*3.75*7.5 nm^3 box--just 
as in Hess' paper Table II, already well equilibrated at 300 K in 
advance; perhaps it is unnecessary to run this double precisely, but I 
was using double precision version (4.5.3.d) just because I forgot to 
switch to the single precision one, however this shouldn't cause the 
problem I had ...)?


Thanks and wish to see your suggestions soon!

Xiang Gu

;Generic mdp file for SPC water equilibration
;Gromacs 4.3.x
;
;T = 300 K
;
;NVT equilibration run, 1.2 ns
;

define   =  ; define here posres etc., e.g. -DPOSRES

integrator  = md
tinit   = 0
dt  = 0.001
nsteps  = 120

; Bond constraints
continuation=  no  ; switch to 'yes' if need to read 
in velocities etc.

constraints =  none; constrain all bond lengths
constraint_algorithm=  lincs   ; default
lincs_order =  4   ; default

; X/V/F/E outputs  change these according to your system 
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog  = 1000
nstenergy   = 1000
; Output frequency and precision for xtc file
nstxtcout   = 1000
xtc-precision   = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps=
; Selection of energy groups
energygrps  = System

; Neighbor list
ns_type  =  grid; neighlist type
nstlist  =  5   ; Freq. to update neighbour list
rlist=  0.9 ; nm (cutoff for short-range NL)
pbc  =  xyz ; xyz(default), no, full(infinite 
systems)

periodic_molecules   =  no

; Non-equilibrium MD
;acc_grps = SYSTEM
cos_acceleration =  0.025   ; PPM option for viscosity 
calculation (nm/ps²)


coulombtype  = PME
rcoulomb = 0.9
optimize_fft = yes ; affects only PME calculations
  ; if you use PME, set also 
rcoulomb = rlist


; van der Waals interactions
vdwtype  =  Cut-off; Van der Waals interactions
rvdw =  0.9; nm (LJ cut-off)
DispCorr =  EnerPres   ; long-range dispersion 
correction to energy and pressure


Tcoupl  = berendsen
tc-grps = System
tau_t   = 2.5
ref_t   = 300.0

;Pressure coupling
Pcoupl  =  no  ; berendsen, tau_p = 1.0 for 
faster equilibration
;Pcoupltype  =  isotropic   ; semi-isotropic: xy and z 
separately (CNT)

;tau_p   =  1.0 ; ps
;compressibility =  4.5e-5  ; 1/bar (water @ 1 atm, 300 K)
;ref_p   =  1.0 ; bar0  4000 1.034798 0.001949

gen_vel = no
;gen_temp= 300.0
;gen_seed= 173529

--
_
Xiang Gu, PhD, Postdoctoral Research Fellow
Department of Applied Physics
Aalto University School of Science and Technology, Finland
Tel: +358-9-470 23137
Email: xiang...@aalto.fi
http://tfy.tkk.fi/soft/ 


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Re: [gmx-users] Viscosity calculations

[Justin A. Lemkul]

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 -f *.edr -s *.tpr -vis option 
and has obtained

a few files such as evisco.xvg, eviscoi.xvg and visco.xvg
The evisco.xvg seems like the one I'm interested, since it has the title as
@title "Shear viscosity using Einstein relation" 
and the unit seems also correct. This file has 5 columns, if I 
understand it correctly(by extrapolating from Hess's paper), the second 
to fourth columns are the results from the off-diagonal elements of the 
pressure
tensor and the fifth one being the average. Hess's paper seems to be 
this one(Figure 5). However, the results are way to low for the ionic 
liquid, since I'm getting 1e-7 kg/m.s and way too low for a ionic liquid.
the eviscoi.xvg file seems to be some kind of integral of evisco.xvg 
which I'm not quite getting what it is.
visco.xvg contains the shear viscosity and bulk viscosity, which again 
seems to be the one I'm looking for. However, the shear viscosity I'm 
looking is(the region which roughly is constant) about 3~5 times higher 
than the experiment. The simulation is 12ns long. Of course, this could 
mean (1) the force field is bad or (2) the Green-kudo converges too 
slowly as Hess pointed out.


Either of these are possible.  Have you tried (1) different parameters or (2) 
longer simulations?  If the model does not reproduce the experiment, it is not a 
very good model...


Since it is not getting any useful result, I turned to non-equilibrium 
MD by applying a shear external force, which is in (2)
(2) I tried both NVT and NPT simulations which uses berendsen coupling 
bath. and set up the cos_acceleration = 0.1 nm/ps^2.
However, I tried to use g_energy -f *edr -s *tpr and by selecting 
the 1/Viscosity or 2CosZ*Vel-X option, the output are giving me zero 
data points on all times.




This could be related to a bug that was fixed just a few days ago.  Try pulling 
the latest stable release from git and trying again.


-Justin

I tried really hard on searching  results on the user list of gromacs 
but it seems that there are quite a lot questions on this but not a 
single satisfactory answer has been given, the most popular answer 
people gave is refer to Hess's paper, but even though Hess was giving a 
good theoretical background on this paper, practically on how to set up 
MD jobs is not given. 
So I would appreciate anyone's hint.


Cheers,

Xiaohu



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Viscosity calculations

[Xiaohu Li]

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 option and has
obtained
a few files such as evisco.xvg, eviscoi.xvg and visco.xvg
The evisco.xvg seems like the one I'm interested, since it has the title as
@title "Shear viscosity using Einstein relation"
and the unit seems also correct. This file has 5 columns, if I understand it
correctly(by extrapolating from Hess's paper), the second to fourth columns
are the results from the off-diagonal elements of the pressure
tensor and the fifth one being the average. Hess's paper seems to be this
one(Figure 5). However, the results are way to low for the ionic liquid,
since I'm getting 1e-7 kg/m.s and way too low for a ionic liquid.
the eviscoi.xvg file seems to be some kind of integral of evisco.xvg which
I'm not quite getting what it is.
visco.xvg contains the shear viscosity and bulk viscosity, which again seems
to be the one I'm looking for. However, the shear viscosity I'm looking
is(the region which roughly is constant) about 3~5 times higher than the
experiment. The simulation is 12ns long. Of course, this could mean (1) the
force field is bad or (2) the Green-kudo converges too slowly as Hess
pointed out.
Since it is not getting any useful result, I turned to non-equilibrium MD by
applying a shear external force, which is in (2)
(2) I tried both NVT and NPT simulations which uses berendsen coupling bath.
and set up the cos_acceleration = 0.1 nm/ps^2.
However, I tried to use g_energy -f *edr -s *tpr and by selecting
the 1/Viscosity or 2CosZ*Vel-X option, the output are giving me zero data
points on all times.

I tried really hard on searching  results on the user list of gromacs but it
seems that there are quite a lot questions on this but not a single
satisfactory answer has been given, the most popular answer people gave is
refer to Hess's paper, but even though Hess was giving a good theoretical
background on this paper, practically on how to set up MD jobs is not
given.
So I would appreciate anyone's hint.

Cheers,

Xiaohu
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[gmx-users] viscosity calculations

[Payman Pirzadeh]

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 almost 100 times bigger than
reported literature. Am I doing something wrong or in the analysis procedure
sth is not divided properly?

Also, I tried to calculate the viscosity through the transverse current
autocorrelation function. The command I issued was:

 

g_tcaf_d_mpi -f 275K_50_50_50_2.trr -s 275K_50_50_50_2.tpr -oc
275K_50_50_50_2 -ov 275K_50_50_50_2 -mol -wt 5 -n watermolecules.ndx

 

The output is:

k  1.253  tau  2.383  eta  0.14641 10^-3 kg/(m s)

irow = 2, icol = 2

  2225392908111942225202360202531386163200.000  -0.195

   0.195   0.000

Numerical Recipes run-time error...

GAUSSJ: Singular Matrix-2

Fit failed!

k  1.253  tau  1.000  eta  0.15845 10^-3 kg/(m s)

k  1.253  tau  0.133  eta  0.44011 10^-3 kg/(m s)

k  1.771  tau  0.455  eta  0.10514 10^-3 kg/(m s)

k  1.771  tau  1.458  eta  0.08329 10^-3 kg/(m s)

k  1.771  tau  0.348  eta  0.13366 10^-3 kg/(m s)

k  1.771  tau  0.324  eta  0.27031 10^-3 kg/(m s)

k  1.771  tau  0.320  eta  0.14002 10^-3 kg/(m s)

k  1.771  tau  2.100  eta  0.07649 10^-3 kg/(m s)

k  2.169  tau  1.541  eta  0.05321 10^-3 kg/(m s)

k  2.169  tau  2.201  eta  0.04949 10^-3 kg/(m s)

irow = 1, icol = 1

   0.000  -0.126

   0.126  708363867825344.750

Numerical Recipes run-time error...

GAUSSJ: Singular Matrix-2

Fit failed!

k  2.169  tau  1.000  eta  0.05282 10^-3 kg/(m s)

k  2.169  tau  0.997  eta  0.07365 10^-3 kg/(m s)

k  2.505  tau  0.511  eta  0.05450 10^-3 kg/(m s)

irow = 1, icol = 1

   0.000   0.710

  -0.710  34533840121856978944.000

Numerical Recipes run-time error...

GAUSSJ: Singular Matrix-2

Fit failed!

k  2.505  tau  1.000  eta  0.03961 10^-3 kg/(m s)

k  2.505  tau  0.248  eta  0.06944 10^-3 kg/(m s)

Averaged over k-vectors:

k  1.253  tau  0.529  Omega  1.189  eta  0.35612 10^-3 kg/(m s)

k  1.771  tau  0.458  Omega  0.832  eta  0.14388 10^-3 kg/(m s)

k  2.169  tau  1.540  Omega  1.601  eta  0.05491 10^-3 kg/(m s)

k  2.505  tau  0.280  Omega  0.499  eta  0.07050 10^-3 kg/(m s)

 

I do not understand the failure parts of the output, also what should I do
with the output numbers?

I took a look at the -ov output. The final 4 numbers are not fittable on a
eta(k)=eta(0)*(1-ak^2). Am I fitting the wrong data?

Sorry for such a huge e-mail.

 

Paymon

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Re: [gmx-users] viscosity calculation_2

[David van der Spoel]

On 2010-09-30 19.36, Payman Pirzadeh wrote:

It does not explain for all files or all columns. For example, in the
evisco.xvg, the following lines are written, but there are 5 columns (one of
which is time). What are the rest? And the unit of the column (written
below) is not clear to me.
@title "Shear viscosity using Einstein relation"
@xaxis  label "Time (ps)"
@yaxis  label "(kg m\S-1\N s\S-1\N)"

Same column are in the eviscoi.xvg (below).
@title "Shear viscosity integral"
@xaxis  label "Time (ps)"
@yaxis  label "(kg m\S-1\N s\S-1\N ps)"

I do not exactly know the relation between the two files and how I should
use them. Also, the enecorr.xvg looks like to be a correlation function. But
its unit is not clear and I do not know how to use it.
I will be appreciated if you could clarify them.
Regards,


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: [gmx-users] viscosity calculation_2

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 VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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RE: [gmx-users] viscosity calculation_2

[Payman Pirzadeh]

It does not explain for all files or all columns. For example, in the
evisco.xvg, the following lines are written, but there are 5 columns (one of
which is time). What are the rest? And the unit of the column (written
below) is not clear to me. 
@title "Shear viscosity using Einstein relation"
@xaxis  label "Time (ps)"
@yaxis  label "(kg m\S-1\N s\S-1\N)"

Same column are in the eviscoi.xvg (below). 
@title "Shear viscosity integral"
@xaxis  label "Time (ps)"
@yaxis  label "(kg m\S-1\N s\S-1\N ps)"

I do not exactly know the relation between the two files and how I should
use them. Also, the enecorr.xvg looks like to be a correlation function. But
its unit is not clear and I do not know how to use it.
I will be appreciated if you could clarify them.
Regards,

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: [gmx-users] viscosity calculation_2

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 VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
-- 
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RE: [gmx-users] viscosity calculation_2

[Dallas Warren]

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 VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
--
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RE: [gmx-users] viscosity calculation_2

[Payman Pirzadeh]

Thanks for the tips.

I just realized that there two other outputs two the g_energy -vis:
evisco.xvg and eviscoi.xvg 
These files contain 5 columns among which the first one looks to be time.
But what are the other 4? What are their differences? 
Regards,

Paymon

-Original Message-
From: 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 comments, It looks like that the third column is the
> appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to
> take the whole trajectory (2 ps) rather than half of the frames. But,
> still g_energy take half of the frames. This has caused improper
convergence
> in viscosity values. If I take only the last 3000 ps (out of 1ps), I
> will get a viscosity of 0.920 with a large rmsd. Is there a bug in
g_energy
> switches?
>
I think this is because it use an autocorrelation function of the 
pressure. By default it uses an FFT to compute it. The ACF at 2 ps 
has very poor statistics (1 data point) and can therefore ruin the 
viscosity. Therefore ACFs by default are plotted to half the traj. There 
is a flag to get a longer (noisier) ACF. g_energy -h might tell you 
which one.

> Payman
>
> -Original 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:
>>
>> 1. My bulk values are fluctuating around 60 (I assume cP). But it looks
> like
>> very weird to me since experimental value for water viscosity is 0.854
cP.
>> My system is at 265K with 4202 molecules. Is sth strange going on? Or I
am
>> missing some unit conversions in the plot.
>>
> Is the experimental value 0.854 at that temperature?
> Could be the the unit is different in the output too. Doesn't it say in
> the xvg file?
>
>> 2. For calculation of protein diffusion constant, should we use the bulk
> or
>> shear viscosity of the solvent (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
>>
>>
>>
>> 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 question.
>>>
>>
>> Plot the output .xvg; you will find it should contain two quantities:
bulk
>> and
>> shear viscosity.
>>
>> -Justin
>>
>>>
>>>
>>> Regards,
>>>
>>>
>>>
>>> Payman
>>>
>>>
>>>
>>>
>>>
>>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] viscosity calculation_2

[David van der Spoel]

On 2010-09-29 22.00, Payman Pirzadeh wrote:

Adding to my previous comments, It looks like that the third column is the
appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to
take the whole trajectory (2 ps) rather than half of the frames. But,
still g_energy take half of the frames. This has caused improper convergence
in viscosity values. If I take only the last 3000 ps (out of 1ps), I
will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy
switches?

I think this is because it use an autocorrelation function of the 
pressure. By default it uses an FFT to compute it. The ACF at 2 ps 
has very poor statistics (1 data point) and can therefore ruin the 
viscosity. Therefore ACFs by default are plotted to half the traj. There 
is a flag to get a longer (noisier) ACF. g_energy -h might tell you 
which one.



Payman

-Original 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:

1. My bulk values are fluctuating around 60 (I assume cP). But it looks

like

very weird to me since experimental value for water viscosity is 0.854 cP.
My system is at 265K with 4202 molecules. Is sth strange going on? Or I am
missing some unit conversions in the plot.


Is the experimental value 0.854 at that temperature?
Could be the the unit is different in the output too. Doesn't it say in
the xvg file?


2. For calculation of protein diffusion constant, should we use the bulk

or

shear viscosity of the solvent (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



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 question.



Plot the output .xvg; you will find it should contain two quantities: bulk
and
shear viscosity.

-Justin




Regards,



Payman













--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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RE: [gmx-users] viscosity calculation_2

[Payman Pirzadeh]

Adding to my previous comments, It looks like that the third column is the
appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to
take the whole trajectory (2 ps) rather than half of the frames. But,
still g_energy take half of the frames. This has caused improper convergence
in viscosity values. If I take only the last 3000 ps (out of 1ps), I
will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy
switches?

Payman

-Original 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:
>
> 1. My bulk values are fluctuating around 60 (I assume cP). But it looks
like
> very weird to me since experimental value for water viscosity is 0.854 cP.
> My system is at 265K with 4202 molecules. Is sth strange going on? Or I am
> missing some unit conversions in the plot.
>
Is the experimental value 0.854 at that temperature?
Could be the the unit is different in the output too. Doesn't it say in 
the xvg file?

> 2. For calculation of protein diffusion constant, should we use the bulk
or
> shear viscosity of the solvent (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
>
>
>
> 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 question.
>>
>
> Plot the output .xvg; you will find it should contain two quantities: bulk
> and
> shear viscosity.
>
> -Justin
>
>>
>>
>> Regards,
>>
>>
>>
>> Payman
>>
>>
>>
>>
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
-- 
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RE: [gmx-users] viscosity calculation

[Payman Pirzadeh]

Apparently, in the file the unit in the file is cP. It might be the case
that I plotted the wrong column. I think I should get the third column.
Regarding the diffusion, I read in papers about rotational diffusion of the
proteins which could be calculated having the viscosity of the liquid and
hydrodynamic volume of the protein. So, volume could be calculated with
radius of gyration + 0.3nm of hydration shell and viscosity is given by
g_energy. So, a rotational diffusion constant could be theoretically
calculated.

Payman



-Original 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:
>
> 1. My bulk values are fluctuating around 60 (I assume cP). But it looks
like
> very weird to me since experimental value for water viscosity is 0.854 cP.
> My system is at 265K with 4202 molecules. Is sth strange going on? Or I am
> missing some unit conversions in the plot.
>
Is the experimental value 0.854 at that temperature?
Could be the the unit is different in the output too. Doesn't it say in 
the xvg file?

> 2. For calculation of protein diffusion constant, should we use the bulk
or
> shear viscosity of the solvent (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
>
>
>
> 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 question.
>>
>
> Plot the output .xvg; you will find it should contain two quantities: bulk
> and
> shear viscosity.
>
> -Justin
>
>>
>>
>> Regards,
>>
>>
>>
>> Payman
>>
>>
>>
>>
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
-- 
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Re: [gmx-users] viscosity calculation

[Warren Gallin]

265 K is -8C, so ice, not liquid water.

That would be more viscous than you might expect.

Waren Gallin

On 2010-09-29, at 12:52 PM, Payman Pirzadeh wrote:

> Well, two questions:
> 
> 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like
> very weird to me since experimental value for water viscosity is 0.854 cP.
> My system is at 265K with 4202 molecules. Is sth strange going on? Or I am
> missing some unit conversions in the plot.
> 
> 2. For calculation of protein diffusion constant, should we use the bulk or
> shear viscosity of the solvent (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] 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 should I do to calculate the viscosity of my 
>> system with these two files? Sorry for such naïve question.
>> 
> 
> Plot the output .xvg; you will find it should contain two quantities: bulk
> and 
> shear viscosity.
> 
> -Justin
> 
>> 
>> 
>> Regards,
>> 
>> 
>> 
>> Payman
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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> 
> 
> 
> --
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> 

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Re: [gmx-users] viscosity calculation

[David van der Spoel]

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 to me since experimental value for water viscosity is 0.854 cP.
My system is at 265K with 4202 molecules. Is sth strange going on? Or I am
missing some unit conversions in the plot.


Is the experimental value 0.854 at that temperature?
Could be the the unit is different in the output too. Doesn't it say in 
the xvg file?



2. For calculation of protein diffusion constant, should we use the bulk or
shear viscosity of the solvent (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



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 question.



Plot the output .xvg; you will find it should contain two quantities: bulk
and
shear viscosity.

-Justin




Regards,



Payman










--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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RE: [gmx-users] viscosity calculation

[Payman Pirzadeh]

Well, two questions:

1. My bulk values are fluctuating around 60 (I assume cP). But it looks like
very weird to me since experimental value for water viscosity is 0.854 cP.
My system is at 265K with 4202 molecules. Is sth strange going on? Or I am
missing some unit conversions in the plot.

2. For calculation of protein diffusion constant, should we use the bulk or
shear viscosity of the solvent (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] 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 should I do to calculate the viscosity of my 
> system with these two files? Sorry for such naïve question.
> 

Plot the output .xvg; you will find it should contain two quantities: bulk
and 
shear viscosity.

-Justin

>  
> 
> Regards,
> 
>  
> 
> Payman
> 
>  
> 
>  
> 

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] viscosity calculation

[Justin A. Lemkul]

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 question.




Plot the output .xvg; you will find it should contain two quantities: bulk and 
shear viscosity.


-Justin

 


Regards,

 


Payman

 

 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] viscosity calculation

[Payman Pirzadeh]

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

 

 

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Re: [gmx-users] Viscosity determination

[David van der Spoel]

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 want to investigate NEMD methods (see Hess, JCP 116 
(2002) 209).




# This file was created Wed Jan  6 16:25:24 2010
# by the following command:
# g_energy -f wfullmdrun_ener.edr -vis viscosity.xvg
#
# g_energy is part of G R O M A C S:
#
# Giant Rising Ordinary Mutants for A Clerical Setup
#
@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"
   0.150.8340840.546697
0.30.883405 0.51992
   0.5999850.9052920.495556
0.799980.9139110.470734
   0.750.9151440.452457
1.199970.9151210.438746
1.399970.9171060.430864
1.599960.9200710.418252
1.799960.9217770.403171
1.50.9189830.394725
2.199950.9181220.387048
2.399940.9233320.383686

Thank you,
Lum




--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] Viscosity determination

[Lum Nforbi]

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
#
# g_energy is part of G R O M A C S:
#
# Giant Rising Ordinary Mutants for A Clerical Setup
#
@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"
  0.150.8340840.546697
   0.30.883405 0.51992
  0.5999850.9052920.495556
   0.799980.9139110.470734
  0.750.9151440.452457
   1.199970.9151210.438746
   1.399970.9171060.430864
   1.599960.9200710.418252
   1.799960.9217770.403171
   1.50.9189830.394725
   2.199950.9181220.387048
   2.399940.9233320.383686

Thank you,
Lum
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Re: [gmx-users] viscosity and acflen in g_energy

[Mark Abraham]

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 trajectory length.


If you read g_energy -h, you will need to specify the ACF length in a 
particular way. If you'd given us your actual command line and some 
information about your trajectory, you might have gotten a definitive 
answer... as it is, we can only assume you made an error of some sort! :-)


Mark
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[gmx-users] viscosity and acflen in g_energy

[Vitaly V. Chaban]

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,
Vitaly
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Re: [gmx-users] Viscosity using periodic perturbation method

[Yanmei Song]

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 than 1%
it will not affect your results significantly."

So technically we should use NVT for the periodic perturbation method,
right? Thanks!

On Tue, May 26, 2009 at 12:03 AM, Berk Hess  wrote:

>  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
> 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
> method. they all used NVT.  I did not found any information about this on
> the manual. Can I use NPT Non-equilibrium MD in order to use periodic
> perturbation method? Thanks in advance!
> --
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>
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-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Re: [gmx-users] Viscosity using periodic perturbation method

[Yanmei Song]

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 speaking it might be incorrect, but since pressure scaling is
usually less than 1%
it will not affect your results significantly."

So technically we should use NVT for the periodic perturbation method,
right? Thanks!

On Tue, May 26, 2009 at 12:03 AM, Berk Hess  wrote:

>  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
> 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
> method. they all used NVT.  I did not found any information about this on
> the manual. Can I use NPT Non-equilibrium MD in order to use periodic
> perturbation method? Thanks in advance!
> --
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>
> ___
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>



-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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RE: [gmx-users] Viscosity using periodic perturbation method

[Berk Hess]

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
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 method. they 
all used NVT.  I did not found any information about this on the manual. Can I 
use NPT Non-equilibrium MD in order to use periodic perturbation method? Thanks 
in advance!

-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University

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[gmx-users] Viscosity using periodic perturbation method

[Yanmei Song]

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 on
the manual. Can I use NPT Non-equilibrium MD in order to use periodic
perturbation method? Thanks in advance!
-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Re: RE: [gmx-users] viscosity calculation using g_energy (3.3.3)

[JMandumpal]

 Dear Berk,

 Thanks for the reply. I have read through your 
paper. I have still some doubts.

When used tcafś  I got files called

tcaf_all.xvg  tcaf_fit.xvg  tcaf.xvg  visc_k.xvg ( all default names).

I think, the file which I should use for fitting, using the formula eta(k) = 
eta (0) (1-ak²) + O(k^4)  the viscoty ( viscosity - k vector plot) is 
visc_k.xvg. Am I right? 

IF yes, what all other files ( tcf_all.xvg, tcaf_fit.xvg and tcaf.xvg) do?

expecting your reply,
Jestin

On Fri, 13 Mar 2009 Berk Hess wrote :
>
>Hi,
>
>I don't understand what you are actually doing now.
>You seem to be mixing multiple methods.
>
>First off all, I would use NPT for all methods, except the one that uses the 
>pressure fluctuation.
>The pressure will have a large effect on the viscosity and if you run NVT you 
>need to have
>exactly the right volume.
>
>If you use the cosine acceleration method, the 1/viscosity is printed in the 
>energy file,
>g_energy will plot it for you.
>
>g_tcaf is only for use with an equilibrium simulation.
>If you read the paper, you will have seen an expression to extrapolate 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,
>
>
>
>   Thank you very much for your 
> appropriate and informative replies.  I tried another method (traverse 
> current method) to calculate the shear viscosity ( a non equilibrium method, 
> which has been described in Berkś paper : Journal of Chemical Physics, 
> 116, page 209 ( Determining the shear viscosity of model liquids from 
> molecular dynamics simulations)),
>
>
>
>I used the g_tcaf utility (ie g_tcaf -f traj1.trr 
> -s binary.tpr -oc test.xvg) . As suggested by David, I increased the system 
> size ( from 500 to 2048 TIP4P molecules). I ran in NVT ensemble which allows 
> the pressure to fluctuate.
>
>Apart from that I added following options to my mdp file, where accelaration 
>of 1A/ps² was given to the system.
>
>
>
>;NON EQUILIBRIUM STUFF
>
>acc_grps  = system
>
>accelerate= 0.1 0.0 0.0
>
>cos_acceleration  = 0.1
>
>
>
>
>
>
>
>Moreover, I saved the trajectory in every 1ps ( so total 500 frames for a 
>500ps simulation)
>
>
>
>then,
>
>
>
>I got the following output:
>
>k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)
>
>k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)
>
>k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)
>
>k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
>
>k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
>
>k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
>
>k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
>
>k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
>
>k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
>
>k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)
>
>k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)
>
>k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)
>
>k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)
>
>k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)
>
>k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)
>
>k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)
>
>
>
>-
>
>
>
>Which shows a strong k dependence over the property: shorter k, better the 
>viscosity, as pointed out in the paper. However, the value obtained is around 
>0.01 times less than the experimental value (1pa-second). Adding to that, the 
>results obtained by this method seems to be very convincing unlike the 
>g_energy that shows a great divergence!!
>
>
>
>So the situation is getting better now. Now, I would like to know whether this 
>can be improved if I save the trajectories more frequently ( 500 fs) and run 
>for longer, say 2ns or change value of accelaration .
>
>
>
>Any thoughts ?
>
>
>
>
>
>regards,
>
>Jes.
>
>
>
>
>
>On Thu, 12 Mar 2009 Berk Hess wrote :
>
> >
>
> >Hi,
>
> >
>
> >This is a very inefficient method for determining the viscosity.
>
> >Also you need really perfect pressure fluctuations: NVT, shifted potentials,
>
> >probably even double precision.
>
> >There was a mail about this recently.
>
> >There are better methods, have a look at:
>
> >http://dx.doi.org/10.1063/1

RE: [gmx-users] viscosity calculation using g_energy (3.3.3)

[Berk Hess]

Hi,

I don't understand what you are actually doing now.
You seem to be mixing multiple methods.

First off all, I would use NPT for all methods, except the one that uses the 
pressure fluctuation.
The pressure will have a large effect on the viscosity and if you run NVT you 
need to have
exactly the right volume.

If you use the cosine acceleration method, the 1/viscosity is printed in the 
energy file,
g_energy will plot it for you.

g_tcaf is only for use with an equilibrium simulation.
If you read the paper, you will have seen an expression to extrapolate 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,



  Thank you very much for your 
appropriate and informative replies.  I tried another method (traverse current 
method) to calculate the shear viscosity ( a non equilibrium method, which has 
been described in Berkś paper : Journal of Chemical Physics, 116, page 209 
( Determining the shear viscosity of model liquids from molecular dynamics 
simulations)),   



   I used the g_tcaf utility (ie g_tcaf -f traj1.trr -s 
binary.tpr -oc test.xvg) . As suggested by David, I increased the system size ( 
from 500 to 2048 TIP4P molecules). I ran in NVT ensemble which allows the 
pressure to fluctuate.

Apart from that I added following options to my mdp file, where accelaration of 
1A/ps² was given to the system.



;NON EQUILIBRIUM STUFF

acc_grps  = system

accelerate= 0.1 0.0 0.0

cos_acceleration  = 0.1







Moreover, I saved the trajectory in every 1ps ( so total 500 frames for a 500ps 
simulation)



then,



I got the following output:

k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)

k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)

k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)

k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)

k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)

k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)

k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)

k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)

k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)

k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)

k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)

k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)

k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)

k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)

k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)

k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)



-



Which shows a strong k dependence over the property: shorter k, better the 
viscosity, as pointed out in the paper. However, the value obtained is around 
0.01 times less than the experimental value (1pa-second). Adding to that, the 
results obtained by this method seems to be very convincing unlike the g_energy 
that shows a great divergence!!



So the situation is getting better now. Now, I would like to know whether this 
can be improved if I save the trajectories more frequently ( 500 fs) and run 
for longer, say 2ns or change value of accelaration . 



Any thoughts ?





regards,

Jes.





On Thu, 12 Mar 2009 Berk Hess wrote :

>

>Hi,

>

>This is a very inefficient method for determining the viscosity.

>Also you need really perfect pressure fluctuations: NVT, shifted potentials,

>probably even double precision.

>There was a mail about this recently.

>There are better methods, have a look at:

>http://dx.doi.org/10.1063/1.1421362

>

>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

>

>

>

>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 bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( 
>Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two 
>order of magnitude. I wonder whether I have done anything wrong while 
>specifying the frequency of saving energy file.

>

>

>

>I have saved the energy file in every 2ps. Isn´t that enough for a simple 
>system like water? OR should I have to save trajectories in every 5fs as 
>suggested by one in a previous post.

>

>

>

>I post the first 20 li

Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)

[JMandumpal]

 Dear Berk and David,

  Thank you very much for your 
appropriate and informative replies.  I tried another method (traverse current 
method) to calculate the shear viscosity ( a non equilibrium method, which has 
been described in Berkś paper : Journal of Chemical Physics, 116, page 209 
( Determining the shear viscosity of model liquids from molecular dynamics 
simulations)),   

   I used the g_tcaf utility (ie g_tcaf -f traj1.trr -s 
binary.tpr -oc test.xvg) . As suggested by David, I increased the system size ( 
from 500 to 2048 TIP4P molecules). I ran in NVT ensemble which allows the 
pressure to fluctuate.
Apart from that I added following options to my mdp file, where accelaration of 
1A/ps² was given to the system.

;NON EQUILIBRIUM STUFF
acc_grps  = system
accelerate= 0.1 0.0 0.0
cos_acceleration  = 0.1



Moreover, I saved the trajectory in every 1ps ( so total 500 frames for a 500ps 
simulation)

then,

I got the following output:
k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)
k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)
k  1.593  tau  1.000  eta  0.09835 10^-3 kg/(m s)
k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
k  2.252  tau  1.000  eta  0.04917 10^-3 kg/(m s)
k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)
k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)
k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)
k  2.759  tau  1.000  eta  0.03278 10^-3 kg/(m s)
k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)
k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)
k  3.185  tau  1.000  eta  0.02459 10^-3 kg/(m s)

-

Which shows a strong k dependence over the property: shorter k, better the 
viscosity, as pointed out in the paper. However, the value obtained is around 
0.01 times less than the experimental value (1pa-second). Adding to that, the 
results obtained by this method seems to be very convincing unlike the g_energy 
that shows a great divergence!!

So the situation is getting better now. Now, I would like to know whether this 
can be improved if I save the trajectories more frequently ( 500 fs) and run 
for longer, say 2ns or change value of accelaration . 

Any thoughts ?


regards,
Jes.


On Thu, 12 Mar 2009 Berk Hess wrote :
>
>Hi,
>
>This is a very inefficient method for determining the viscosity.
>Also you need really perfect pressure fluctuations: NVT, shifted potentials,
>probably even double precision.
>There was a mail about this recently.
>There are better methods, have a look at:
>http://dx.doi.org/10.1063/1.1421362
>
>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
>
>
>
>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 bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( 
>Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two 
>order of magnitude. I wonder whether I have done anything wrong while 
>specifying the frequency of saving energy file.
>
>
>
>I have saved the energy file in every 2ps. Isn´t that enough for a simple 
>system like water? OR should I have to save trajectories in every 5fs as 
>suggested by one in a previous post.
>
>
>
>I post the first 20 lines of the output file.
>
>
>
>---
>
>
>
># This file was created Thu Mar 12 16:20:09 2009
>
># by the following command:
>
># g_energy -f water.edr -vis test.xvg
>
>#
>
># g_energy is part of G R O M A C S:
>
>#
>
># GROup of MAchos and Cynical Suckers
>
>#
>
>@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"
>
>1.99203  9.6633 96.3893
>
>3.98406

RE: [gmx-users] viscosity calculation using g_energy (3.3.3)

[Berk Hess]

Hi,

This is a very inefficient method for determining the viscosity.
Also you need really perfect pressure fluctuations: NVT, shifted potentials,
probably even double precision.
There was a mail about this recently.
There are better methods, have a look at:
http://dx.doi.org/10.1063/1.1421362

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 



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 bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( 
Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two 
order of magnitude. I wonder whether I have done anything wrong while 
specifying the frequency of saving energy file.



I have saved the energy file in every 2ps. Isn´t that enough for a simple 
system like water? OR should I have to save trajectories in every 5fs as 
suggested by one in a previous post.



I post the first 20 lines of the output file.



---



# This file was created Thu Mar 12 16:20:09 2009

# by the following command:

# g_energy -f water.edr -vis test.xvg 

#

# g_energy is part of G R O M A C S:

#

# GROup of MAchos and Cynical Suckers

#

@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"

   1.99203  9.6633 96.3893

   3.98406 11.1625 98.1365

5.9761 12.6631  99.838

   7.96813 13.4652 101.366

   9.96016 13.7012 100.249

-





regards,

Jes



On Thu, 12 Mar 2009 David van der Spoel wrote :

>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 corresponding xvg file is  (kJ mol\S-1\N). I 
>> think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. 
>> Then why is this discrepancy.? Or did I make any mistake?

>>

>Mu is the dipole (in Debye). The units of these things are incorrect for 
>everything that is not an energy. This will be fixed in the next gmx version. 
>g_energy -h tells you what to do:

>

>g_energy -f ener -vis viscosity

>

>>

>>--I give the command on the prompt:

>>

>>g-energy -f ener.edr - o viscosity.xvg ;

>>then chose option 40 ( Mu-X).

>>

>>system details:

>>**

>>My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at 
>>150K, the ensemble is NPT. The version I am using is 3.3.3








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Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)

[JMandumpal]

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 bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( 
Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two 
order of magnitude. I wonder whether I have done anything wrong while 
specifying the frequency of saving energy file.

I have saved the energy file in every 2ps. Isn´t that enough for a simple 
system like water? OR should I have to save trajectories in every 5fs as 
suggested by one in a previous post.

I post the first 20 lines of the output file.

---

# This file was created Thu Mar 12 16:20:09 2009
# by the following command:
# g_energy -f water.edr -vis test.xvg 
#
# g_energy is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@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"
   1.99203  9.6633 96.3893
   3.98406 11.1625 98.1365
5.9761 12.6631  99.838
   7.96813 13.4652 101.366
   9.96016 13.7012 100.249
-


regards,
Jes

On Thu, 12 Mar 2009 David van der Spoel wrote :
>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 corresponding xvg file is  (kJ mol\S-1\N). I 
>> think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. 
>> Then why is this discrepancy.? Or did I make any mistake?
>>
>Mu is the dipole (in Debye). The units of these things are incorrect for 
>everything that is not an energy. This will be fixed in the next gmx version. 
>g_energy -h tells you what to do:
>
>g_energy -f ener -vis viscosity
>
>>
>>--I give the command on the prompt:
>>
>>g-energy -f ener.edr - o viscosity.xvg ;
>>then chose option 40 ( Mu-X).
>>
>>system details:
>>**
>>My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at 
>>150K, the ensemble is NPT. The version I am using is 3.3.3
___
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Re: [gmx-users] viscosity calculation using g_energy (3.3.3)

[David van der Spoel]

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 corresponding xvg file is  (kJ 
mol\S-1\N). I think GROMACS uses SI unit , which is Pa-Second in the 
case of viscosity. Then why is this discrepancy.? Or did I make any mistake?


Mu is the dipole (in Debye). The units of these things are incorrect for 
everything that is not an energy. This will be fixed in the next gmx 
version. g_energy -h tells you what to do:


g_energy -f ener -vis viscosity



--I give the command on the prompt:

g-energy -f ener.edr - o viscosity.xvg ;
then chose option 40 ( Mu-X).

system details:
**
My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds 
at 150K, the ensemble is NPT. The version I am using is 3.3.3





regards,
Jes



Shopping 






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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] viscosity calculation using g_energy (3.3.3)

[JMandumpal]

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 is  (kJ mol\S-1\N). I think 
GROMACS uses SI unit , which is Pa-Second in the case of viscosity. Then why is 
this discrepancy.? Or did I make any mistake?


--I give the command on the prompt:

g-energy -f ener.edr - o viscosity.xvg ; 
then chose option 40 ( Mu-X).

system details:
**
My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at 
150K, the ensemble is NPT. The version I am using is 3.3.3




regards,
Jes___
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Re: [gmx-users] Viscosity in PE

[Berk Hess]

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 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 equation 
(friction=6 x PI x visc x radius). But you need to have saved the 
velocities fairly often (say every 5 fs?). This came up recently in the 
mailing lists, you can search the velocity autocorrelation function. This 
method integrates the integral at time infinite (ie, see Morriss and 
Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the 
web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or 
might not be a good approximation for your system. Otherwise you can do 
more sophisticated methods such as those outlined in chapter 6 of the 
manual.

Hope it helps,
Esther


An alternative method that is implemented requires non-equibrium 
simulations. Check out


@Article{Hess2002b,
  author =   {B. Hess},
  title = 	 {Determining the shear viscosity of model liquids from 
molecular simulation},

  journal =  {J. Chem. Phys.},
  year = 2002,
  volume =   116,
  pages ={209-217}
}

you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2


In Gromacs viscosity calculations can be done with several methods,
all of which are described in the paper mentioned above.

But for PE-1000 it is not that straightforward as for a simple liquid.
The system has very long relaxation times and the viscosity will be
very non-linear in the shear rate.
You should read some literature on viscosity calculations in polymer melts.

Berk.


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RE: [gmx-users] Viscosity in PE

[Alessandro Mattozzi]

Thanx!

Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden



-Original Message-
From: [EMAIL PROTECTED] on behalf of Berk Hess
Sent: Fri 9/8/2006 8:34 AM
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] 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:
>>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 equation 
>>(friction=6 x PI x visc x radius). But you need to have saved the 
>>velocities fairly often (say every 5 fs?). This came up recently in the 
>>mailing lists, you can search the velocity autocorrelation function. This 
>>method integrates the integral at time infinite (ie, see Morriss and 
>>Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the 
>>web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or 
>>might not be a good approximation for your system. Otherwise you can do 
>>more sophisticated methods such as those outlined in chapter 6 of the 
>>manual.
>>Hope it helps,
>>Esther
>
>An alternative method that is implemented requires non-equibrium 
>simulations. Check out
>
>@Article{Hess2002b,
>   author = {B. Hess},
>   title =  {Determining the shear viscosity of model liquids from 
>molecular simulation},
>   journal ={J. Chem. Phys.},
>   year =   2002,
>   volume = 116,
>   pages =  {209-217}
>}
>
>you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2

In Gromacs viscosity calculations can be done with several methods,
all of which are described in the paper mentioned above.

But for PE-1000 it is not that straightforward as for a simple liquid.
The system has very long relaxation times and the viscosity will be
very non-linear in the shear rate.
You should read some literature on viscosity calculations in polymer melts.

Berk.


___
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<>___
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Re: [gmx-users] Viscosity in PE

[Berk Hess]

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 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 equation 
(friction=6 x PI x visc x radius). But you need to have saved the 
velocities fairly often (say every 5 fs?). This came up recently in the 
mailing lists, you can search the velocity autocorrelation function. This 
method integrates the integral at time infinite (ie, see Morriss and 
Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the 
web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or 
might not be a good approximation for your system. Otherwise you can do 
more sophisticated methods such as those outlined in chapter 6 of the 
manual.

Hope it helps,
Esther


An alternative method that is implemented requires non-equibrium 
simulations. Check out


@Article{Hess2002b,
  author =   {B. Hess},
  title = 	 {Determining the shear viscosity of model liquids from 
molecular simulation},

  journal =  {J. Chem. Phys.},
  year = 2002,
  volume =   116,
  pages ={209-217}
}

you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2


In Gromacs viscosity calculations can be done with several methods,
all of which are described in the paper mentioned above.

But for PE-1000 it is not that straightforward as for a simple liquid.
The system has very long relaxation times and the viscosity will be
very non-linear in the shear rate.
You should read some literature on viscosity calculations in polymer melts.

Berk.


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Re: [gmx-users] Viscosity in PE

[David van der Spoel]

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 be 
calculated using Stoke's equation (friction=6 x PI x visc x radius). But 
you need to have saved the velocities fairly often (say every 5 fs?). 
This came up recently in the mailing lists, you can search the velocity 
autocorrelation function. This method integrates the integral at time 
infinite (ie, see Morriss and Evan's book /Statistical Mechanics of 
Nonequilibrium Liquids, /now on the web @ 
http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or might 
not be a good approximation for your system. Otherwise you can do more 
sophisticated methods such as those outlined in chapter 6 of the manual.

Hope it helps,
Esther


An alternative method that is implemented requires non-equibrium 
simulations. Check out


@Article{Hess2002b,
  author =   {B. Hess},
  title = 	 {Determining the shear viscosity of model liquids from 
molecular simulation},

  journal =  {J. Chem. Phys.},
  year = 2002,
  volume =   116,
  pages ={209-217}
}

you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2



Esther Caballero-Manrique
Guenza Group
University of Oregon
Eugene, OR
usa
541-346-2485
Alessandro Mattozzi wrote:




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 Mattozzi



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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] Viscosity in PE

[Esther Caballero-Manrique]

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 equation (friction=6 x PI x visc x radius). But 
you need to have saved the velocities fairly often (say every 5 fs?). 
This came up recently in the mailing lists, you can search the velocity 
autocorrelation function. This method integrates the integral at time 
infinite (ie, see Morriss and Evan's book /Statistical Mechanics of 
Nonequilibrium Liquids, /now on the web @ 
http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or might 
not be a good approximation for your system. Otherwise you can do more 
sophisticated methods such as those outlined in chapter 6 of the manual.

Hope it helps,
Esther

Esther Caballero-Manrique
Guenza Group
University of Oregon
Eugene, OR
usa
541-346-2485
Alessandro Mattozzi wrote:




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 Mattozzi



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[gmx-users] Viscosity in PE

[Alessandro Mattozzi]

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 Mattozzi




___
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Please don't post (un)subscribe requests to the list. Use the 
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