Thanks a lot.
Regards
El 18 may. 2017 8:38 AM, "David A Case" <david.case.rutgers.edu> escribió:
> On Wed, May 17, 2017, Carlos Romero wrote:
>
> > I want to know how changes the response of one protein when it is in
> > diferent pH.
> >
> > My know about Molecular Dynamics is that resulting trajectories are the
> > possibles conformations of a molecule after being applied some energy,
> many
> > of them are not possible because wrong conformations, but some of them
> are
> > probably right. Among these structures, is one with the lowest potential
> > energy, which is the most probably in nature.
>
> This is not correct. There are always thermal fluctuations, and an
> equilibrated MD simulation should sample the correct distribution. There
> are
> no "right" or "wrong" conformations, just ones that occur more frequently
> or
> less frequently.
>
> If you wish to extract snapshots from MD simulations, say to perform a
> docking
> calculation, it would be more realistic to choose random ones (and
> certainly
> more than one), than to choose the frame with the lowest potential energy.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 18 2017 - 20:30:03 PDT
