Re: [gmx-users] Interpretation of MSD

[Gaurav Goel]

Dear Akash,

For local equilibration, your simulation time should be at least equal
to Brownian relaxation time ~ a^2/D, where 'a' is particle radius and
D is the 3D diffusion coefficient. This would imply that your MSD
should be at least .6 * a^2.

Some other possible checks:
i. Make sure MSD versus t is linear at long times. Alternatively,
check that MSD / t is showing a plateau at long times.

Regards,
G

Gaurav Goel, PhD
Assistant Professor
Department of Chemical Engineering
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi 110016
India


On Thu, Jun 29, 2017 at 9:32 PM, Pandya, Akash
 wrote:
> Hi all,
>
> I performed Mean Square Deviation for my ligand molecules in x, y, z 
> directions in order to obtain the diffusion coefficients. From my 
> understanding, the square root of the highest MSD value should be significant 
> enough to interpret that the ligand molecules have in fact moved enough 
> during the course of the simulation. This may seem like an ambiguous 
> question, but what would you deem a suitable value for MSD, for diffusion 
> coefficients to be appropriate to measure?
>
> Many thanks,
>
> Akash
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[gmx-users] Interpretation of MSD

[Pandya, Akash]

Hi all,

I performed Mean Square Deviation for my ligand molecules in x, y, z directions 
in order to obtain the diffusion coefficients. From my understanding, the 
square root of the highest MSD value should be significant enough to interpret 
that the ligand molecules have in fact moved enough during the course of the 
simulation. This may seem like an ambiguous question, but what would you deem a 
suitable value for MSD, for diffusion coefficients to be appropriate to measure?

Many thanks,

Akash
-- 
Gromacs Users mailing list

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