Dear Christoph, Thank you for your answer. I am getting to be clear.
The following is the extrapolated potential using csg_call. As you see in the attached pictures, the force is constant in the extrapolated regions. It means that the potentials extrapolated by csg_call are linear instead of cubic or something else. Does the constant force is normal by Boltzmann Inversion followed by csg_call for extrapolation? The reason to extrapolate correctly the potentials is due to performing IBI for non-bonded potentials/. Thank you. On Mon, May 2, 2016 at 4:51 PM, Christoph Junghans <[email protected]> wrote: > 2016-05-02 13:16 GMT-06:00 Chang Woon Jang <[email protected]>: > > Dear Christopher, > > > > So, do I need to extrapolate Force separately? > No, the forces are in the xvg file already, csg_call does everything > you need to use the table with gromacs. And anyhow you also wouldn't > extrapolate the force independently of the potential. > > Christoph > > > > 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. > > 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. 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