[gmx-users] Potential energy

[Alex]

Dear all,

The potential energy of my system after two minimization steps (with and
without constrained) is converging well, however, it is still positive
around 1000 kj/mol !
I think it is not a good sign for my system, but, what could be the reason
and how I can overcome the issue? The system generated via "gmx
insert-molecules" contains 1000 molecules of "C21H28O4".

Second question;
To calculate the RDF between pair of atoms, let's say A and B, I was
wondering if those two atoms should be differentiated in index.ndx file
from beginning before invoking the gmx gromps?(similar to energygrps) or
one can does the simulation without index.ndx and still possible to
calculate the RDF between those two atoms?

Thank you.

Regards,
Alex