Hello,<br><br>I am simulating two carbon nanotubes in water. <br>1.The
two nanotubes are facing each other, end to end, with their end bonded
with polymers.<br>2. I bonded heavy (molecular weight=100000) dummy
atoms to the carbon atoms of the nanotubes, so that they won't move.
Each bond length is initially 0, and spring constant k=2000 kJ/mol.<br>
3. I simulated the two tubes in water and calculated their interaction
force through the spring extension. Then I calculated the energy of the
mean force.<br><br>Is the energy free energy or internal energy? Thanks.
I am using NVT with PDB.<br>
If it is free energy, is it Gibbs or Helmholtz?<br><br>I am a little
puzzled by the entropy.<br>Because I am trying to tabulate this energy
vs. distance and use the table as input for another larger scale Monte
Carlo simulation. However, if it is the free energy (containing the
entropy), then when I applied it to the MC, which automatically include
the entropy consideration, will I mis-calculate the free energy during
the MC simulation (Seems I may double the entropy effect or neutralize
it )? Hope I make myself clear.<br>
<br>Thanks,<br>Young