what is the difference between msd and chunk/msd command

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1

Hi all

I want to calculate the CH4 molecule displacement on surface. But I am bit confuse about msd and chunk/msd command. Could any one please explain me the difference between those command and which will be preferable for my system.

thank you

Anderson

2

Hi all

I want to calculate the CH4 molecule displacement on surface. But I am bit
confuse about msd and chunk/msd command.

Could any one please explain me the difference between those command and

which will be preferable for my system.

compute msd works on individual atoms (and averages over them), ​compute
msd/chunk over chunks instead.
neither computes the "displacement", though, but a "mean squared
displacement". to compute the displacement, you could to use fix store
state and then define an atom style variable to compute the displacement
for individual atoms and then average over them. for CH4 using the carbon
atoms only is a very good approximation, if you are not using a united atom
model already.

axel.

3

Dear Axel

Thank you very much for your suggestion.

Since I want to calculate the change of the diffusion coefficient at different condition, hence MSD will be right calculation for me because the slope of MSD will be directly proportional to the diffusion coefficient.

From your suggestion I suppose, If I make a group for the carbon of CH4 molecules and calculate msd by this command will fine

group carbon type 1

compute MSD carbon msd 500
fix 1 carbon ave/time c_MSD file msd.txt mode vector

Its might be OK?

Thank you

Anderson

4

Dear Axel

Thank you very much for your suggestion.

Since I want to calculate the change of the diffusion coefficient at
different condition, hence MSD will be right calculation for me because the
slope of MSD will be directly proportional to the diffusion coefficient.

From your suggestion I suppose, If I make a group for the carbon of CH4
molecules and calculate msd by this command will fine

group carbon type 1

compute MSD carbon msd 500
fix 1 carbon ave/time c_MSD file msd.txt mode vector

Its might be OK?

​please do what every scientist should do in the case of not being certain
about whether something works as expected.
construct a simple test case, where you ​know the result and see whether
your hypothesis for a solution works for this. then try something more
complex while checking whether the results are consistent until you can try
out your target system with (deserved confidence).
what if i tell you it is OK, but i am wrong? or a nasty SOB?

axel.

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