Dear Christopher, Thank you for your detailed instruction. Does this csg_call also extrapolate the force associated with potential?
Thank you. Best regards, Changwoon Jang On Mon, May 2, 2016 at 2:56 PM, Christoph Junghans <[email protected]> wrote: > 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. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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