Skip to main content

Thermostating only a few atoms in MD

Submitted by prasad matukumilli on
research
MD
Berendsen

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

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

Mon, 06/30/2008 - 01:51 Permalink