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From: wei <lwstudy.sina.com>

Date: Wed, 28 Dec 2016 10:07:51 +0800

Thanks for answering, Jing.

I have wrote a program to calculate the translational diffusion constant by myself (I used center of mass of sugar, but I also tested only with coordinates of sugar), but I get different MSD values comparing with ptraj's result. When I calculate the MSD for only one atom in the sugar molecule, I found the MSD values (in the second column) for x axes obtained from ptraj (also only for this atom) is about 3.73-fold larger than what I calculated. So I was wondering if the MSD values from ptraj have been scaled.

While using cpptraj to calculate D, I also want to know whether we should image atoms. According to my test, image and noimage give two totally different results. In Amber16 user manual, it is said that 'In order to correctly calculate diffusion molecules should take continuous paths, so imaging of atoms is autoimatically performed.' This is quite confusing. Because If we wrap the atoms back into box, how can we calculate the real mean square displacement? Because we might underestimate the movement of the molecule.

Any suggestions? Thanks in advance for your help!

Regards,Liu Wei

--------------------------------

----- ÔÊ¼ÓÊ¼þ -----

·¢¼þÈË£ºHuang Jing <jing.huang8911.gmail.com>

ÊÕ¼þÈË£ºlwstudy.sina.com, AMBER Mailing List <amber.ambermd.org>

Ö÷Ìâ£ºRe: [AMBER] Distance diffusion calculation in ptraj and cpptraj

ÈÕÆÚ£º2016Äê12ÔÂ27ÈÕ 21µã04·Ö

Hello,I am still a beginner of amber ; the unit of MSD would be Angstrom^2 ;in my opinion, no scaling factor is for mean square displacement and "2n n=3" is needed for the calculation of diffusion coefficient; the calculated diffusion coefficient is the "sug_O[Slope]/2n" n=3,Perhaps my answer is not all correct and you need to examine them,as I am still a beginner,I followed up the official amber tutorial : http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml

jing

Dr. Jing HuangInstitute of Chemistry and the Lise Meitner-Minerva Center for Computational QuantumChemistry, Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem 91904, Israel

On Tue, Dec 27, 2016 at 9:58 AM, wei <lwstudy.sina.com> wrote:

Dear all,

I want to calculate distance diffusion coefficient D for a sugar molecule in bulk water. I have tried ptraj and cpptraj analysis tools to realize this calculation respectively.

After running the ptraj script, I got five output files (diff.dat_x.xmgr, diff.dat_y.xmgr, diff.dat_z.xmgr, diff.dat_r.xmgr, diff.dat_a.xmgr). Let me display few lines of data deposited in diff.dat_r.xmgr:

3990.000 1990.5193992.000 2023.4453994.000 1913.1503996.000 1941.7723998.000 1964.5964000.000 1982.162

1. What does the second column represent and what are their unit? It seems that the second column lists MSD values, but have it been scaled by a factor (for instance, 2n, n=3 in the case of r)?

Let me also paste the calculated D-values by cpptraj:

#Set sug_O[D] sug_O[Slope] sug_O[Intercept] sug_O[Corr] sug_O[Label] 1 0.3546 0.2128 521.8718 0.7209 sug_O_AvgDr 2 0.4605 0.0921 -145.4334 0.6208 sug_O_AvgDx 3 0.3895 0.0779 492.8230 0.5437 sug_O_AvgDy 4 0.2138 0.0428 174.4822 0.5268 sug_O_AvgDz

2. I was wondering what is the unit of the calculated D values on the second column?

Thanks in advance!

Regards,Liu Wei

--------------------------------

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

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Received on Tue Dec 27 2016 - 18:30:03 PST

Date: Wed, 28 Dec 2016 10:07:51 +0800

Thanks for answering, Jing.

I have wrote a program to calculate the translational diffusion constant by myself (I used center of mass of sugar, but I also tested only with coordinates of sugar), but I get different MSD values comparing with ptraj's result. When I calculate the MSD for only one atom in the sugar molecule, I found the MSD values (in the second column) for x axes obtained from ptraj (also only for this atom) is about 3.73-fold larger than what I calculated. So I was wondering if the MSD values from ptraj have been scaled.

While using cpptraj to calculate D, I also want to know whether we should image atoms. According to my test, image and noimage give two totally different results. In Amber16 user manual, it is said that 'In order to correctly calculate diffusion molecules should take continuous paths, so imaging of atoms is autoimatically performed.' This is quite confusing. Because If we wrap the atoms back into box, how can we calculate the real mean square displacement? Because we might underestimate the movement of the molecule.

Any suggestions? Thanks in advance for your help!

Regards,Liu Wei

--------------------------------

----- ÔÊ¼ÓÊ¼þ -----

·¢¼þÈË£ºHuang Jing <jing.huang8911.gmail.com>

ÊÕ¼þÈË£ºlwstudy.sina.com, AMBER Mailing List <amber.ambermd.org>

Ö÷Ìâ£ºRe: [AMBER] Distance diffusion calculation in ptraj and cpptraj

ÈÕÆÚ£º2016Äê12ÔÂ27ÈÕ 21µã04·Ö

Hello,I am still a beginner of amber ; the unit of MSD would be Angstrom^2 ;in my opinion, no scaling factor is for mean square displacement and "2n n=3" is needed for the calculation of diffusion coefficient; the calculated diffusion coefficient is the "sug_O[Slope]/2n" n=3,Perhaps my answer is not all correct and you need to examine them,as I am still a beginner,I followed up the official amber tutorial : http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml

jing

Dr. Jing HuangInstitute of Chemistry and the Lise Meitner-Minerva Center for Computational QuantumChemistry, Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem 91904, Israel

On Tue, Dec 27, 2016 at 9:58 AM, wei <lwstudy.sina.com> wrote:

Dear all,

I want to calculate distance diffusion coefficient D for a sugar molecule in bulk water. I have tried ptraj and cpptraj analysis tools to realize this calculation respectively.

After running the ptraj script, I got five output files (diff.dat_x.xmgr, diff.dat_y.xmgr, diff.dat_z.xmgr, diff.dat_r.xmgr, diff.dat_a.xmgr). Let me display few lines of data deposited in diff.dat_r.xmgr:

3990.000 1990.5193992.000 2023.4453994.000 1913.1503996.000 1941.7723998.000 1964.5964000.000 1982.162

1. What does the second column represent and what are their unit? It seems that the second column lists MSD values, but have it been scaled by a factor (for instance, 2n, n=3 in the case of r)?

Let me also paste the calculated D-values by cpptraj:

#Set sug_O[D] sug_O[Slope] sug_O[Intercept] sug_O[Corr] sug_O[Label] 1 0.3546 0.2128 521.8718 0.7209 sug_O_AvgDr 2 0.4605 0.0921 -145.4334 0.6208 sug_O_AvgDx 3 0.3895 0.0779 492.8230 0.5437 sug_O_AvgDy 4 0.2138 0.0428 174.4822 0.5268 sug_O_AvgDz

2. I was wondering what is the unit of the calculated D values on the second column?

Thanks in advance!

Regards,Liu Wei

--------------------------------

_______________________________________________

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 Tue Dec 27 2016 - 18:30:03 PST

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