[gmx-users] Potential or total energy in dhdl files

[Александр Лашков]

Thank you for anwer, but i don't understand this. For BAR this terms not
necessary. But for MBAR i'am not sure. In third party program - alchemlyb
and alchemystry-analysis, total energy or potential used for calculate
reduced potential if this terms include in dhdl files.
Sincerely,
Alexander

ср, 4 дек. 2019 г. в 12:02, Alessandra Villa <
alessandra.villa.biosim at gmail.com>:

> HI,
>
> On Tue, Dec 3, 2019 at 3:56 PM Александр Лашков <alashkov83 at gmail.com>
> wrote:
>
> > Dear gromacs team, you wrote in documentation "This information is needed
> > for later free energy analysis if the states of interest are at different
> > temperatures. If all states are at the same temperature, this information
> > is not needed. ‘potential’ is useful in case one is using mdrun -rerun to
> > generate the dhdl.xvg file.". But reduced potential used for MBAR
> analysis
> > include energy term and pV (for Gibs energy for NPT-ensemble) and
> chemical
> > potential (for grand canonical ensemble). All the same, is it necessary
> or
> > not necessary to save energy in dhdh files?
> >
>
> You do not need the  mdp option "dhdl-print-energy"  if you are performing
> free energy calculation at one temperature.
>
> Best regards
> Alessandra
>
>
>
> > Sincerely,
> > Alexander Lashkov
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.