2016-05-02 12:29 GMT-06:00 Chang Woon Jang <[email protected]>: > 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? You need to create an xml file with the addition options, like this: $ cat options.xml <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>2.0</table_end> <table_bins>0.002</table_bins> </gromacs> </inverse> </cg>
After that: $ csg_call --options options.xml --ia-type bond --ia-name bond convert_potential gromacs table_b3.xvg full_table_b3.xvg will works and generate full_table_b3.xvg, which is the extrapolated table you need. Christoph > > > 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. -- 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.
