Dear Christoph,
I mean the file written by csg_boltzmann with Tab command. If
csg_boltzmann used GROMACS units, I think the second column (energy) in
KJ/mol, and the third column (force) in KJ/mol-nm. Am I right?
In lammps I will use, the energy should be Kcal/mol and the force should be
Kcal/mol-Angstrom.
Therefore, I would like to make sure that the file units from csg_boltzmann
Tab use KJ/mol and KJ/mol-nm.
If I am wrong, please correct me.
Thank you.
Best regards,
Changwoon Jang
On Tue, Dec 22, 2015 at 6:30 PM, Christoph Junghans <[email protected]>
wrote:
> 2015-12-22 15:56 GMT-07:00 Chang Woon Jang <[email protected]>:
> > Dear Christoph,
> >
> > Thank you, Christoph. I have one more question. I ran an atomistic
> > simulation in GROMACS.
> >
> > Are the units written in the file KJ/mol and KJ/mol-nm for energy and
> force,
> > respectively?
> Yes & no, csg_boltzmann uses Gromacs units.
> While csg_inverse uses nm and the rest depends on what you use for
> k_B*T in the settings file.
>
> However, lammps can do simulation in nm as well, see the
> spce/ibi_lammps example:
> <https://github.com/votca/csg-tutorials/tree/master/spce/ibi_lammps>
>
> Christoph
> >
> > I need to convert and format the energy and force for Lammps simulation.
> >
> > Thank you.
> >
> > Best regards,
> > Changwoon Jang
> >
> >
> > On Tue, Dec 22, 2015 at 5:44 PM, Christoph Junghans <[email protected]>
> > wrote:
> >>
> >> 2015-12-22 15:04 GMT-07:00 Chang Woon Jang <[email protected]>:
> >> > Dear Votca Users,
> >> >
> >> > I have used csg_boltzmann with "tab" command to write the
> >> > Boltzmann-inverted potential.
> >> >
> >> > It gives three columns. In the manual, the format of the file is
> >> > described
> >> > in sec 3.6. It states that "Those tables generally have the format
> >> >
> >> > x y [error] flag
> >> >
> >> > where x is input quantity (e.g. radius, angle), y is the computed
> >> > quantity
> >> > (e.g. a potential) and [error] is an optional error for y."
> >> >
> >> > However, I do not believe that the third column is error because when
> I
> >> > draw
> >> > the third column as a function of radius (the first column) is much
> much
> >> > bigger than the second column. Also, there is no flag.
> >> >
> >> > Is this still correct format of Boltzmann-inverted potential file from
> >> > Tab
> >> > command of csg_boltzmann as described in Votca Manual?
> >> csg_boltzmann uses a different format for table than csg_inverse (sec.
> >> 3.6).
> >> csg_boltzmann writes the force in 3rd column.
> >>
> >> Cheers,
> >>
> >> Christoph
> >> >
> >> > I attached the figure for you.
> >> >
> >> > --
> >> > Best regards,
> >> > Changwoon Jang,
> >> >
> >> > --
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> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
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> Christoph Junghans
> Web: http://www.compphys.de
>
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