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.
