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<br>