Dear David,
Thank you for the prompt reply.
Chetna
On Thu, Sep 14, 2017 at 5:11 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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
>
>
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--
Best wishes
Chetna
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Received on Thu Sep 14 2017 - 09:00:04 PDT
