2016-08-29 14:37 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > 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 That command is wrong as you don't convert a bond. For bonds, the minimum for the xvg table will always be set to 0.
> > > > > 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 convert_potential takes a VOTCA table (in rad) not a xvg table. VOTCA table have 3 columns, angle(rad), potential(in simulation units), flag (i/o/u) The lines which have valid point should have an "i", but in case of doubt you can just leave the 3rd column empty. Christoph > > > 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 <jungh...@votca.org> > wrote: >> >> 2016-08-29 14:08 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> > 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, >> > >> > -- >> > 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 votca+unsubscr...@googlegroups.com. >> > To post to this group, send email to votca@googlegroups.com. >> > 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 votca+unsubscr...@googlegroups.com. >> To post to this group, send email to votca@googlegroups.com. >> 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: cj...@drexel.edu > > -- > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
