Hi Oliver,
first, note that Amber11 now contains data collection for the MBAR
estimator on some free energy calculations as an option. With runs already
completed, it is not so simple.
If you saved your trajectories quite often, you could rerun (imin=5) all
trajectories with all intermediate prmtop-files and collect the total
system energies. This requires enough mdcrd-snapshots, plus a way to build
intermediate prmtop files (simple for charges, very hard vor vdW-changes).
Other than that, I see no good way to get the energy values you need.
Kind Regards,
Thomas
On Tue, May 4, 2010 4:32 am, Oliver Kuhn wrote:
> Hi everybody,
>
> I would like to use the MBAR estimator on data from a TI run.
> For estimating with MBAR, I do not need only the dV/dl values of
> snapshots t of states l (that have been written to the mdout-files) but
> all the potential energy values of snapshots t of states l EVALUATED AT
> STATES l (before differentiating).
> Is there a way to "restore" these values?
>
> Thanks for any help.
>
> Greets,
> Oliver
>
> --
> Dipl.-Bioinf. Oliver Kuhn, Department of Bioinformatics,
> Center for Medical Biotechnology, University of Duisburg-Essen,
> Universitätsstr. 1-5, 45141 Essen, Germany
> phone +49 201 183-3121, oliver.kuhn.uni-due.de
>
>
>
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue May 04 2010 - 02:30:03 PDT
