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From: Vijay Manickam Achari <vjrajamany.yahoo.com>

Date: Fri, 26 Jul 2013 03:42:48 +0100 (BST)

Dear Dickson,

Thanks for your kind reply.

I almost done of what you have prescribed. By the way, I would like to know about the unit for this.

As explained by on-screen information during ptraj run as below:

"DIFFUSION

Only the average results will be dumped to diffusion-malto-thermo63.dat_?.xmgr

The time between frames in psec is 5.000.

To calculated diffusion constants, calculate the slope of the lines(s)

and multiply by 10.0/6.0; this will give units of 1x10**-5 cm**2/s

The atoms in the calculation follow: :63"

Should I times factor "1x10**-5" to the answer I get ? Is that is the way of doing?

Regards

Vijay Manickam Achari

(Phd Student c/o Prof Rauzah Hashim)

Chemistry Department,

University of Malaya,

Malaysia

vjramana.gmail.com

________________________________

From: "Dickson, Callum" <callum.dickson09.imperial.ac.uk>

To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>

Sent: Thursday, 25 July 2013, 18:39

Subject: Re: [AMBER] Calculating diffusion Constant D

Hi Vijay,

So from the ambertools manual:

<filename_root>_x.xmgr Mean square displacement(s) in the X direction.

<filename_root>_y.xmgr Mean square displacement(s) in the Y direction.

<filename_root>_z.xmgr Mean square displacement(s) in the Z direction.

<filename_root>_a.xmgr Average mean square displacement(s).

<filename_root>_r.xmgr Total distance travelled.

Assuming your bilayer is aligned along the z-axis, sum the x- and y- plots to get MSD in the xy-plane and take the slope of the resulting graph, then multiply the gradient by (10/4) to get the diffusion coefficient. Also note that you should do simulations in the NVE ensemble if you want to compare resulting diffusion values to experiment.

All the best,

Callum

________________________________________

From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Vijay Manickam Achari [vjrajamany.yahoo.com]

Sent: 25 July 2013 11:07

To: Amber mailing List; Amber Scrops

Subject: [AMBER] Calculating diffusion Constant D

Dear amber experts,

I need some clarification on calculating the diffusion constant D from MD simulation for bilayer system using "diffusion" command in ptraj.

The command I used is :

"diffusion :1-1 5.0 average diffusion-malto-thermo1.dat"

I get to see information saying that

"DIFFUSION

Only the average results will be dumped to diffusion-malto-thermo63.dat_?.xmgr

The time between frames in psec is 5.000.

To calculated diffusion constants, calculate the slope of the lines(s)

and multiply by 10.0/6.0; this will give units of 1x10**-5 cm**2/s

The atoms in the calculation follow: :63"

I get five files. I choose the file with *z extention to calculate the gradient.

For this I used gnuplot with command below:

" f(x) = b + m*x "

" fit f(x) "allxy-mal-cel-iso-bcm-diffusion_z.dat" using 1:2 via b,m "

I get values for "b" and "m" as below:

======================= ==========================

b = 1.12224 +/- 0.003892 (0.3468%)

m = 0.0337373 +/- 0.0001686 (0.4997%)

This means I get the gradient value as "0.0337373" and the y-intercept as "1.12224".

For now I want to calculate the diffusion.

So I times 0.0337373 with (10/4) since mine is bilayer (2 dimensional system).

I get "0.08434325".

Finally should I write my answer as

0.08434325 x 10^(-5) cm^2/s

Is this is the correct way of interpret the D value?

I appreciate anyone's reply to this post.

Vijay Manickam Achari

(Phd Student c/o Prof Rauzah Hashim)

Chemistry Department,

University of Malaya,

Malaysia

vjramana.gmail.com

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jul 25 2013 - 20:00:03 PDT

Date: Fri, 26 Jul 2013 03:42:48 +0100 (BST)

Dear Dickson,

Thanks for your kind reply.

I almost done of what you have prescribed. By the way, I would like to know about the unit for this.

As explained by on-screen information during ptraj run as below:

"DIFFUSION

Only the average results will be dumped to diffusion-malto-thermo63.dat_?.xmgr

The time between frames in psec is 5.000.

To calculated diffusion constants, calculate the slope of the lines(s)

and multiply by 10.0/6.0; this will give units of 1x10**-5 cm**2/s

The atoms in the calculation follow: :63"

Should I times factor "1x10**-5" to the answer I get ? Is that is the way of doing?

Regards

Vijay Manickam Achari

(Phd Student c/o Prof Rauzah Hashim)

Chemistry Department,

University of Malaya,

Malaysia

vjramana.gmail.com

________________________________

From: "Dickson, Callum" <callum.dickson09.imperial.ac.uk>

To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>

Sent: Thursday, 25 July 2013, 18:39

Subject: Re: [AMBER] Calculating diffusion Constant D

Hi Vijay,

So from the ambertools manual:

<filename_root>_x.xmgr Mean square displacement(s) in the X direction.

<filename_root>_y.xmgr Mean square displacement(s) in the Y direction.

<filename_root>_z.xmgr Mean square displacement(s) in the Z direction.

<filename_root>_a.xmgr Average mean square displacement(s).

<filename_root>_r.xmgr Total distance travelled.

Assuming your bilayer is aligned along the z-axis, sum the x- and y- plots to get MSD in the xy-plane and take the slope of the resulting graph, then multiply the gradient by (10/4) to get the diffusion coefficient. Also note that you should do simulations in the NVE ensemble if you want to compare resulting diffusion values to experiment.

All the best,

Callum

________________________________________

From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Vijay Manickam Achari [vjrajamany.yahoo.com]

Sent: 25 July 2013 11:07

To: Amber mailing List; Amber Scrops

Subject: [AMBER] Calculating diffusion Constant D

Dear amber experts,

I need some clarification on calculating the diffusion constant D from MD simulation for bilayer system using "diffusion" command in ptraj.

The command I used is :

"diffusion :1-1 5.0 average diffusion-malto-thermo1.dat"

I get to see information saying that

"DIFFUSION

Only the average results will be dumped to diffusion-malto-thermo63.dat_?.xmgr

The time between frames in psec is 5.000.

To calculated diffusion constants, calculate the slope of the lines(s)

and multiply by 10.0/6.0; this will give units of 1x10**-5 cm**2/s

The atoms in the calculation follow: :63"

I get five files. I choose the file with *z extention to calculate the gradient.

For this I used gnuplot with command below:

" f(x) = b + m*x "

" fit f(x) "allxy-mal-cel-iso-bcm-diffusion_z.dat" using 1:2 via b,m "

I get values for "b" and "m" as below:

======================= ==========================

b = 1.12224 +/- 0.003892 (0.3468%)

m = 0.0337373 +/- 0.0001686 (0.4997%)

This means I get the gradient value as "0.0337373" and the y-intercept as "1.12224".

For now I want to calculate the diffusion.

So I times 0.0337373 with (10/4) since mine is bilayer (2 dimensional system).

I get "0.08434325".

Finally should I write my answer as

0.08434325 x 10^(-5) cm^2/s

Is this is the correct way of interpret the D value?

I appreciate anyone's reply to this post.

Vijay Manickam Achari

(Phd Student c/o Prof Rauzah Hashim)

Chemistry Department,

University of Malaya,

Malaysia

vjramana.gmail.com

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jul 25 2013 - 20:00:03 PDT

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