Thanks Jason, you clarified everything...
Yi
On Tue, Jul 23, 2013 at 7:08 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Jul 23, 2013 at 5:53 PM, Yi An <anyiphysics.gmail.com> wrote:
>
> > Hi guys,
> >
> > With your help I successfully ran multiple trajectory binding energy
> > calculation using MMPBSA.py. However, the binding energy from multiple
> > trajectory calculation is four times bigger than the binding energy from
> > single trajectory calculation. After I checked the output files, I found
> > that in the multiple trajectory calculation, the complex's G gas and the
> > receptor's G gas is only 1/10 of G gas in single trajectory calculation.
> It
> > looks like almost all other energy terms are the same. So I'm really
> > confused here. If anyone can answer my question I would be very grateful.
> > Thanks.
> >
>
> In the single trajectory approach, the internal potential terms (i.e., the
> bonded terms) cancel completely since the bound and unbound conformations
> are identical -- only the nonbonded terms will differ. As a result, the
> terms that cancel exactly are omitted from the calculation and their
> contribution is not included in any of the terms.
>
> The internal potential terms are the bond, angle, torsion (and
> urey-bradley, CMAP, and impropers for CHARMM force fields), as well as the
> 1-4 electrostatic and 1-4 vdW terms. Those last two can be very large. If
> you set verbose=2 in the &general section of the MMPBSA.py input file, it
> will add these contributions back in.
>
> For multiple trajectories, this cancellation does not occur, and so each
> term is included by default. As a note, any internal terms that do NOT
> cancel in the single trajectory approach are printed and trigger a warning
> in the output file (regardless of the verbose value).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Jul 23 2013 - 18:00:02 PDT
