On Thu, Sep 14, 2017, Chetna Tyagi wrote:
>
> I simulated a peptide for 100 ns and upon mdout_analyzer.py analysis found
> that the Etot (Total energy) remains positive and equal to EKtot (kinetic
> energy). This was an implicit simulation. The resultant structure is
> expected and no problems arose there.
>
> Of course that means that the potential energy of the system (EPtot) did
> not contribute to the energy of the system and it almost remains at zero
> throughout.
>
> The kinetic energy and total energy overlap each other in the graph
> attached below.
>
> The energy remains positive all throughout. Is it normal?
The absolute values of potential energies are of little interest. Whether
the average potential energy is positive or negative depends a lot on the size
and sequence. You should look instead at secondary structure (for example),
or for *changes* in potential energies (which are relevant). The sort of
plots you have made so far are just the beginning: establshing that you
seem to have a stable simulation (but not much more).
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 14 2017 - 08:30:04 PDT
