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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Thu, 31 Aug 2017 09:03:18 -0400

Hi,

On Wed, Aug 30, 2017 at 6:51 PM, carmine marco morgillo

<FnTcy.hotmail.it> wrote:

*> Averaging the values of column#5 I would get the right hand of the Einstein equation (?).
*

The average is over particles, not time. The numbers being reported in

the output of 'stfcdiffusion' are averaged over selected atoms each

time step. To understand how to calculate the diffusion constant via

the Einstein relation it may help to think of an alternate

formulation:

2*n*D = lim(t->inf.)[MSD/t]

So what you need to get the diffusion coefficient is MSD vs. time. The

most common way to get this is to calculate the slope of the best-fit

line for MSD vs. time (you can do this in cpptraj with the 'regress'

Analysis command, or use your favorite math package/plotting program).

Then divide by 2*n (where n is the number of dimensions) and multiply

by 10.0 to convert from units of Ang^2/ps to cm^2/s. There is a

discussion of this in the cpptraj section of the Amber manual (28.9.21

diffusion). The calculation of the diffusion constant can be done

automatically by the 'diffusion' command but not yet by

'stfcdiffusion' (I'm working on eventually merging all the

functionality of the two commands).

Note also that diffusion in membrane systems can be a little trickier

to calculate properly, and you need to correct for periodic boundary

conditions and the very anisotropic nature of lipid diffusion. Rich

Pastor et al. have done a lot of interesting work in this area; see

e.g. http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b09111 and

references therein.

Hope this helps,

-Dan

Date: Thu, 31 Aug 2017 09:03:18 -0400

Hi,

On Wed, Aug 30, 2017 at 6:51 PM, carmine marco morgillo

<FnTcy.hotmail.it> wrote:

The average is over particles, not time. The numbers being reported in

the output of 'stfcdiffusion' are averaged over selected atoms each

time step. To understand how to calculate the diffusion constant via

the Einstein relation it may help to think of an alternate

formulation:

2*n*D = lim(t->inf.)[MSD/t]

So what you need to get the diffusion coefficient is MSD vs. time. The

most common way to get this is to calculate the slope of the best-fit

line for MSD vs. time (you can do this in cpptraj with the 'regress'

Analysis command, or use your favorite math package/plotting program).

Then divide by 2*n (where n is the number of dimensions) and multiply

by 10.0 to convert from units of Ang^2/ps to cm^2/s. There is a

discussion of this in the cpptraj section of the Amber manual (28.9.21

diffusion). The calculation of the diffusion constant can be done

automatically by the 'diffusion' command but not yet by

'stfcdiffusion' (I'm working on eventually merging all the

functionality of the two commands).

Note also that diffusion in membrane systems can be a little trickier

to calculate properly, and you need to correct for periodic boundary

conditions and the very anisotropic nature of lipid diffusion. Rich

Pastor et al. have done a lot of interesting work in this area; see

e.g. http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b09111 and

references therein.

Hope this helps,

-Dan

-- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Aug 31 2017 - 06:30:03 PDT

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