Dear Christoph,
What I have used is the following command with the options.xml file.
<cg>
<bonded>
<!-- name of the interaction -->
<name>dihedral</name>
<min>0.285</min>
<max>0.615</max>
<step>0.001</step>
</bonded>
<inverse>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>3.14</table_end>
<table_bins>0.001</table_bins>
</gromacs>
</inverse>
</cg>
csg_call --options options.xml --ia-type bond --ia-name dihedral
convert_potential gromacs table_d1.xvg full_table_d1.xvg
This gives only from 0 to 3.14. When I used the following command, it gives
error.
csg_call --options options.xml --ia-type dihedral --ia-name dihedral
convert_potential gromacs table_d1.xvg full_table_d1.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 123
do_external - linenumber 22 (see 'csg_call --cat function
do_external')
die - linenumber 2 (see 'csg_call --cat function die')
#################################################################################################################
#
#
#
ERROR:
#
# do_external:
subscript
#
# /home/chang/PACKAGE/votca/share/votca/scripts/inverse/table_linearop.pl
--on-x table_d1.xvg table_d1.pot.scale.Jdqcv 57.2957795 0 #
# (from tags table linearop)
failed
#
# Details can be found
above
#
#
#
##################################################################################################################
On Mon, Aug 29, 2016 at 4:27 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-08-29 14:08 GMT-06:00 Chang Woon Jang <[email protected]>:
> > Dear Votca Users,
> >
> >
> > Dihedral potential obtained from is range -3.14 to 3.14. I would
> like to
> > convert it to gromacs format using csg_call. How do I make options.xml
> file?
> What is the csg_call command you are running?
> Do you use the "--ia-type dihedral" option to specify you are
> converting a dihedral?
>
> Christoph
> > When I use the following xml file, it only produce from 0 to 3.14 not
> -3.14.
> >
> > <cg>
> > <bonded>
> > <!-- name of the interaction -->
> > <name>bond</name>
> > <min>0.285</min>
> > <max>0.615</max>
> > <step>0.001</step>
> > </bonded>
> > <inverse>
> > <gromacs>
> > <pot_max>1e8</pot_max>
> > <table_end>3.14</table_end>
> > <table_bins>0.001</table_bins>
> > </gromacs>
> > </inverse>
> > </cg>
> >
> > Thank you.
> >
> >
> > Best regards,
> > Changwoon Jang,
> >
> > --
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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--
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]
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