Dear Christopher, I have type the command as you wrote. I have the following bond potential named "table_b3.xvg". Therefore,
$ csg_call convert_potential gromacs table_b3.xvg table.xvgRunning
subscript 'potential_to_gromacs.sh table_b3.xvg table.xvg' (from tags
convert_potential gromacs) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Convert table_b3.xvg to table.xvg
Callstack:
/home/chang/PACKAGE/votca/bin/csg_call - linenumber 199
do_external - linenumber 176 in
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/functions_common.sh
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/potential_to_gromacs.sh
- linenumber 84
csg_get_interaction_property - linenumber 33 (see 'csg_call
--cat function csg_get_interaction_property')
die - linenumber 2 (see 'csg_call --cat function die')
###############################################################################################################
#
#
#
ERROR:
#
# csg_get_interaction_property: bondtype is undefined (when calling from
csg_call set it by --ia-type option) #
# Details can be found
above
#
#
#
###############################################################################################################
Then, I included --ia-type bond, but the error still occurred.
Callstack:
/home/chang/PACKAGE/votca/bin/csg_call - linenumber 199
do_external - linenumber 176 in
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/functions_common.sh
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/potential_to_gromacs.sh
- linenumber 107
csg_get_property - linenumber 8 (see 'csg_call --cat function
csg_get_property')
die - linenumber 2 (see 'csg_call --cat function die')
#####################################################################################################
#
#
#
ERROR:
#
# csg_get_property: CSGXMLFILE is undefined (when calling from csg_call set
it by --options option) #
# Details can be found
above
#
#
#
#####################################################################################################
Would you tell me how to fix the problem?
I also included the bond potential, table_b3.xvg.
but the following error occurred.
Thank you.
Best regards,
Changwoon Jang
On Mon, May 2, 2016 at 1:14 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-05-02 10:48 GMT-06:00 Chang Woon Jang <[email protected]>:
> > Dear VOTCA users,
> >
> > I obtained bond potential using Boltzmann Inversion and then
> extrapolated
> > the potential using csg_resample.
> >
> > The obtained bond potential is saved as bondpot.png and the extrapolated
> > potential is saved as Extrapolated.png in the attachment.
> >
> > As you see in the low r, the extrapolated bond potential is going to the
> > negative. I do not think that the potential is going to negative like
> this
> > in the lower r value. In the obtained potential (bondpot.png), the
> minimum
> > is around 0.42 nm.
> >
> > Do I need to fix this potential or do I miss something to do right
> > extrapolation?
> The original potential looks great. It seems to me that a simple convert
> using:
> $ csg_call convert_potential gromacs table.pot table.xvg
> should do it?
>
> Can you shared that original potential with us? (the pot file not the
> png or xvg)
> Can you explain a bit more in detail what you did to extrapolate the
> potential?
>
> Thanks,
>
> Christoph
> >
> >
> >
> > Best regards,
> > Changwoon Jang,
> >
> > --
> > You received this message because you are subscribed to the Google Groups
> > "votca" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to [email protected].
> > To post to this group, send email to [email protected].
> > Visit this group at https://groups.google.com/group/votca.
> > For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [email protected].
> To post to this group, send email to [email protected].
> Visit this group at https://groups.google.com/group/votca.
> For more options, visit https://groups.google.com/d/optout.
>
--
Best regards,
Changwoon Jang,
Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104
Voice: (662) 617-2267
E-mail: [email protected]
--
You received this message because you are subscribed to the Google Groups
"votca" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at https://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.
table_b3.xvg
Description: Binary data
