[gmx-users] Add new window for MBAR calculation

[Alessandra Villa]

Hi,

Just a suggestion.
On Wed, Dec 11, 2019 at 7:17 AM Александр Лашков <alashkov83 at gmail.com>
wrote:

> Dear colleagues. I use the MBAR algorithm to process the results of an
> alchemical conversion in GROMACS. If I find a bad states overlaps, is it
> possible to add a new window  without fully recomputind MD simulation for
> all windows?
>

For MBAR, I am not so sure, since one use information from all the lambda
points. But for BAR it should be enough to to run again only the
neighbouring points.

If you have trajectories (saved frequently enough) for the original points,
you could run only the extra lambda points and then do rerun to compute the
energy values  needed for the  script (used for MBAR).

Best regards
Alessandra





> Best regards,
> Alexander Lashkov
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