If I see it correctly in
https://github.com/votca/csg/blob/master/share/scripts/inverse/potential_shift.pl#L82,
for bonded interactions the shift value is determined as the lowest
potential value which e.g. for a quadratic potential would be the minimum:
for(my $i=0; $i<=$#r; $i++) {
$zero=$dpot[$i] if (($flag[$i] =~ /[i]/) and not defined($zero));
$zero=$dpot[$i] if (($flag[$i] =~ /[i]/) and ($dpot[$i]<$zero));
}
However, in this case the lowest potential value is -47041495963199 at 1.5
Am Dienstag, 23. April 2019 17:14:35 UTC+2 schrieb Christoph Junghans:
>
> On Tue, Apr 23, 2019 at 9:02 AM <[email protected] <javascript:>>
> wrote:
> >
> > Hi,
> >
> > as I see it the default --shift option in the table conversion causes
> the problem (it shifts all potential values by the 10^14) factor as you
> have very high forces and thus potential energies at the "left" border of
> your table.
>
> Thanks, that was a good catch! I am wondering isn't the potential for
> angle interactions suppose to shift so that the minimum is at 0?
> Code here:
>
> https://github.com/votca/csg/blob/master/share/scripts/inverse/potential_shift.pl#L82
>
>
> So where does it go wrong?
>
> Christoph
> >
> > I tried the following commands and it seems to work:
> >
> >
> > csg_call table integrate A-B-A.force A-B-A.pot
> > csg_call table linearop A-B-A.pot A-B-A.pot -1 0
> >
> > csg_call --ia-type angle --ia-name A-B-A --options
> settings_convert_table_angles.xml convert_potential lammps --no-shift
> --clean A-B-A.pot A-B-A.table
> >
> > with the settings file I attached.
> >
> > The --no-shift option prevents the unwanted shifting.
> >
> > (As I see it, in case you want to run the simulation with lammps you
> should scale your potential file A-B-A.pot before! you call the
> "convert_potential lammps" command as this command outputs the table in the
> right format and converted to degrees, but does not correct for the
> different units in GROMACS and LAMMPS. Though, if you use lammps units real
> (energy kcal/mol, .... )you have to scale the potential values by 0.239006
> before by e.g. runninh
> >
> > csg_call table linearop A-B-A.pot A-B-A.pot_scaled 0.239006 0
> >
> > and then running
> >
> > csg_call --ia-type angle --ia-name A-B-A --options
> settings_convert_table_angles.xml convert_potential lammps --no-shift
> --clean A-B-A.pot_scaled A-B-A.table
> >
> > afterwards)
> >
> > Best
> >
> > Christoph
> >
> >
> >
> > Am Donnerstag, 18. April 2019 16:07:10 UTC+2 schrieb
> [email protected]:
> >>
> >> Hi,
> >>
> >> I have been trying to integrate forces and convert potential to lammps
> .pot format. I used all the appropriate script but after the conversion to
> lammps the potential for angles seem unreasonable.
> >> Very high energy values. Something seems to be going wrong with
> potential_shift.pl. I would be grateful if you could share your insights
> on this.
> >>
> >> Best regards,
> >> Christianna
> >>
> >> ps. The same thing seems to be happening with Gromacs angle potentials.
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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