I tried to perform a simple energy minimization of nanotube with water molecules in it. The initial psf and pdb files are taken from the NAMD's nanotube tutorial. After I ran the energy minimization, the potential energy converged to the positive value which shouldn't have been the case. I've attached here with both configuration for minimization as well as output log file of energy minimization.
Hi Roshan,
I am not a user of NAMD, but it seems to me that as long as the harmonic force constant of the potential energy is positive you are in a potential well. As you might recall, only the relative values between energy states are experimentally verifiable (physically meaningful). You need to see if the difference between two energy states are what you expect for an IR band or enthalpy change. I most often get a total energy that is positive for a molecular mechanics calculation. Hopefully this gets to the root of your question.
Thanks Ramin. I did, but it's still not converging to a negative value. Infact. it is only converging to positive potential no matter how much I increase the minimization step number.
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