[gmx-users] potential energy

[Bogdan Costescu]

On Fri, Jan 16, 2015 at 2:56 PM, mah maz <mahmaz71 at gmail.com> wrote:
> These potential energies are the average ones, how can I get the final
> potential of the system?

In the log file you get instantaneous values for all types of
calculated energies. You can also get it with g_energy, but you'd have
to read a bit more about its options :)

> Are average potentials good terms to decide if the
> simulation was wrong?

They can be, if you know what to expect. But you have to compare
apples with apples - a comparison of CNT plus some solvent to a
protein in water is not relevant. Furthermore, the force field that
you choose can make a big difference...

> Can the positive potentials be the effect of forcefield inappropriate files?

Only you can decide that :) We have no idea what force field you have
used and whether that force field is appropriate for what you intend
to do.

The truncated Morse potential we have developed for graphene does
result in positive potentials. In general, most/all potentials for
graphene/CNTs result in positive potential energies as the Coulomb
term is missing. This is due to the fact that the Coulomb term can't
possibly model the coupled while also very mobile electrons in
graphene/CNTs, and is normally just left undefined.

> The system is a CNT containing some solvent. Can positive potentials be the
> reflection of the system's angle pressure not willing to reform from plane
> graphene system?

I can't quite understand the last sentence. You mention your system is
a CNT, but now you talk about graphene and reformation. Are you hoping
to roll/unroll between graphene and CNTs???

Cheers,
Bogdan