2016-08-29 14:47 GMT-06:00 Christoph Junghans <jungh...@votca.org>: > 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> Btw, this seems to be wrong. Or do you only want to use the value from 0.285 to 0.615 to become part of the xvg table?
VOTCA distinguishes between regions to sample (given by min and max) and regions to extrapolate (-pi to +pi for dihedrals), which are specified below. >> <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 -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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