Dear Christopher, So, do I need to extrapolate Force separately?
Best regards, Changwoon Jang On Mon, May 2, 2016 at 3:14 PM, Christoph Junghans <[email protected]> wrote: > 2016-05-02 13:04 GMT-06:00 Chang Woon Jang <[email protected]>: > > Dear Christopher, > > > > Thank you for your detailed instruction. Does this csg_call also > > extrapolate the force associated with potential? > The force is calculated after the extrapolation happened, csg_call > actually only reads potential column of the input table. > > Christoph > > > > 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. > > 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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