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From: Mathy Froeyen <Matheus.Froeyen_at_rega.kuleuven.ac.be>

Date: Wed 26 May 1999 11:05:23 +0200

Hello Amber users,

My troubles with the calculation of the water diffusion coefficient from

the slope of the mean-square displacement correlation function is a

matter of including enough statistics.

First of all, there is no problem with my Amber PME trajectories.

The problem is in the simple program I wrote myself, which calculates

the correlation function.

I did not keep track of periodic conditions. I supposed this was not

necesesary, because I would only include waters moving close to the

solute in the center of the box, and at short times ( < 10 ps).

After a suggestion from Thomas Cheatham, I found that in my calculation,

because I do eliminate periodic conditions, I do not have enough

molecules in the calculation to get good statistics. That's why my

correlation curve moves up when I increase the radius around the solute

to include more bulk waters. The curve does not get worse but better! Of

course I could not make this radius too high because then I would get

serious problems with periodicity.

(The purpose of this radius is to investigate the influence of the

solute on the solvent diffusion, see for instance in the book Proteins,

Brooks, Karplus, & Pettitt 1988 p. 155).

I have to adapt my program to include periodicity to increase statistics

in my calculation (or I have to do longer MD simulations).

The high velocities for some molecules I found, I suppose they are

normal if you consider a Gaussian distribution around an average

velocity at 300K.

Thanks to all who responded,

Mathy Froeyen

Received on Wed May 26 1999 - 02:05:23 PDT

Date: Wed 26 May 1999 11:05:23 +0200

Hello Amber users,

My troubles with the calculation of the water diffusion coefficient from

the slope of the mean-square displacement correlation function is a

matter of including enough statistics.

First of all, there is no problem with my Amber PME trajectories.

The problem is in the simple program I wrote myself, which calculates

the correlation function.

I did not keep track of periodic conditions. I supposed this was not

necesesary, because I would only include waters moving close to the

solute in the center of the box, and at short times ( < 10 ps).

After a suggestion from Thomas Cheatham, I found that in my calculation,

because I do eliminate periodic conditions, I do not have enough

molecules in the calculation to get good statistics. That's why my

correlation curve moves up when I increase the radius around the solute

to include more bulk waters. The curve does not get worse but better! Of

course I could not make this radius too high because then I would get

serious problems with periodicity.

(The purpose of this radius is to investigate the influence of the

solute on the solvent diffusion, see for instance in the book Proteins,

Brooks, Karplus, & Pettitt 1988 p. 155).

I have to adapt my program to include periodicity to increase statistics

in my calculation (or I have to do longer MD simulations).

The high velocities for some molecules I found, I suppose they are

normal if you consider a Gaussian distribution around an average

velocity at 300K.

Thanks to all who responded,

Mathy Froeyen

Received on Wed May 26 1999 - 02:05:23 PDT

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