[gmx-users] Add new window for MBAR calculation

[Александр Лашков]

Thank you very much.
Alexander

пт, 13 дек. 2019 г. в 11:30, Alessandra Villa <
alessandra.villa.biosim at gmail.com>:

> 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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