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Thermostating only a few atoms in MD

I am trying to apply Berendsen thermostat for CNT. When I choose to leave one third of the tube atoms to evolve freely with out distrubing the momentum, I am unable to acheive the target temperature and further temperature increases gradually over the whole simulation run (even with a thermostat parameter equals to the timestep i.e., like a simple scaling). How it is possible to acheive target temperature,by scaling only a part of atoms, using some scaling value which should actually scales all the atoms momenta. Is there any other parameter which decides the number of scaling atoms and/or to modify the scaling factor to acheive target temp.? Prasad MVD.


Adrian S. J. Koh's picture

Hi Prasad,

I have performed MD simulations on NVT ensembles.  I need to clarify the
following with you:

1.   Exactly how many atoms did you thermostated?

2.   How did you take care of the kinematics of the atoms at the interface
between the thermostated and un-thermostated atomic layers?

3.   I think you are aware that, by partially thermostating your CNT, you are
handling an MD problem with mixed ensembles (NVT & NVE).  Hybrid
ensembles frequently leads to incorrect physical properties inferred from the
atomic data.  Did you account for the mixed ensemble in the statistical
mechanical sense?

4.   I gather that you are trying to obtain a target temperature for the
entire CNT by thermostating two-thirds of the CNT.  Correct me if I am wrong. 
But if I read it correctly, may I ask, why are you doing this?  It didn't seem
physically possible to thermostat a part of the problem and expect the entire
problem to approach the targeted temperature.

Thank you.


Adrian KSJ

Try Langevin dynamics. It's probably the best thermostat for small systems.

Prasad MVD

What MD program do you use? If it's home-made,  you need to do
some coding (of course, know the theory first). Langevin dynamics can
be found everywhere: any MD book, or simply google.

Also, if possible, try to thermostat the atoms in the outer layer .

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