The problem with sander is that it can't sample the end-points but
rather only points up to 0.005 away (so the range is 0.005 to 0.995).
This necessarily means that there would be some missing energies and
thus some error if you only did MBAR analysis over that range. Sander
could principally estimate the MBAR end-point energies but proper
BAR/MBAR requires explicit sampling of all lambda points. The latter is
also a problem because the namelist variables bar_l_* only allow you to
set up an equally spaced array.
What is the lambda range you are look at?
Overall I don't know if there is a useful scheme to support this type
of analysis for sander. That's why I have decided to not support it.
On Tue, 15 Dec 2015 15:42:18 +0100
Johannes Loeffler <johannes.r.loeffler.gmail.com> wrote:
> Thank you for your fast answer!
> I just seem to run into another problem;
>
> Note: BAR/MBAR results are not computed.
>
> is printed out whenever I try to run the script. I used the sander
> module of AMBER 14. Might that be a problem?
>
> Thanks again Johannes
>
> On 12/15/2015 02:46 PM, Hannes Loeffler wrote:
> > https://github.com/MobleyLab/alchemical-analysis
> >
> > or better yet my fork which has a few more bug fixes
> >
> > https://github.com/halx/alchemical-analysis
> >
> >
> > On Tue, 15 Dec 2015
> > 14:36:06 +0100 Johannes Loeffler <johannes.r.loeffler.gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> I am trying to perform mbar analysis and was wondering if there are
> >> any tutorials on how to extract the output from amber out files. In
> >> the simulations ifmbar=1 flag was naturally included!
> >>
> >> Thanks for your input
> >>
> >> Joe
> >>
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Received on Tue Dec 15 2015 - 07:30:04 PST
