iMechanica - Berendsen - Comments

What MD program do you use?

Lianqing Zheng — Mon, 30 Jun 2008 10:20:49 -0400

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 .

Using Langevin thermostat..how can I..

prasad_nano — Mon, 30 Jun 2008 10:11:55 -0400

Prasad MVD

Langevin

Lianqing Zheng — Mon, 30 Jun 2008 09:40:52 -0400

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

Questions for you

Adrian S. J. Koh — Sun, 29 Jun 2008 21:51:57 -0400

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