In general, the more snapshots used the better binding energy in order to
obtain a proper average of all the system's conformations. Although after a
certain numbers (I have found 200 to usually be the "magic" number) of
snapshots the average binding energy usually changes very little. This will
change based on your specific system and the conformations that it visits
during the MD simulation. However, you shouldn't be getting such drastically
different binding energies using 20 snapshots versus 5 (or 1) snapshots.
They should be pretty close to the same. I would suggest that something is
occurring during the extraction of the coordinate snapshots.
-Bill
On Wed, Jun 16, 2010 at 9:56 PM, kamlesh sahu <kamleshsemail.gmail.com>wrote:
> Dear Dr. Bill,
>
> Is there some rule like how many snapshots should be extracted for 2 ns of
> simulation (my case for example=2 ns of production MD) ?
> Is this inconsistency, the result of less number of snapshot. I also tried
> with just one snapshot and 5 snapshots and binding energy in both cases was
> -41kcal/mol (looks correct).
>
> Thank you
> Regards,
>
> On Thu, Jun 17, 2010 at 10:49 AM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > Usually this high of a binding energy is indicative of an inconsistency
> > between the prmtop files and the coordinates in the generated snapshots.
> I
> > would suggest trying to visualize the snapshots with the prmtop files and
> > make sure those are consistent.
> >
> > Good luck!
> >
> > -Bill
> >
> > On Wed, Jun 16, 2010 at 9:45 PM, kamlesh sahu <kamleshsemail.gmail.com
> > >wrote:
> >
> > > Hi all,
> > >
> > > I am running binding energy calculations using MMPBSA on amber 10.
> > > Previously I was getting some error messages which were solved when I
> > used
> > > fillratio=4.0. Now I finished the calculation but the binding energy
> > seems
> > > abnormally high. First I extracted 20 snapshots using the command
> > >
> > > $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
> > > then I run the command
> > >
> > > $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa_Example >
> > > extract_coords_Example.log
> > > I get a binding energy of -37091150.59 kcal/mol. (please see attached
> > > 20-snaps_statistics.out and other input and log files)
> > > Could somebody tell me what part of calculation I am possibly making
> > > mistake
> > > in ?
> > >
> > > Thank you
> > > Regards,
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Kamlesh Kumar Sahu (post doc researcher)
> Riken, wako, Saitama, JAPAN
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Jun 16 2010 - 19:30:05 PDT
