[gmx-users] trjconv : error

[Yan Gao]

Hello,

I am simulating two carbon nanotubes in water.
1.The two nanotubes are facing each other, end to end, with their end bonded
with polymers.
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.
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.

Is the energy free energy or internal energy? Thanks. I am using NVT with
PDB.
If it is free energy, is it Gibbs or Helmholtz?

I am a little puzzled by the entropy.
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.

Thanks,
Young
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