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

[Alessandra Villa]

Hi,

On Wed, Dec 4, 2019 at 11:39 AM Александр Лашков <alashkov83 at gmail.com>
wrote:

> 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,
>

I am not familiar with these third party programs.  If those programs read
as input  dhdl.xvg file and
they require the values of total and potential energy to be written in the
dhdl.xvg.
Then you can activate the option in mdp according to which information the
program requires to have in the dhdl file.

Potential and total energy in GROMACS are generally stored in edr file and
written log file, the mdp option  "dhdl-print-energy" gives an extra option
to have those values written in the dhdl.xvg file.

Best regards
Alessandra





> 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
> > > --
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