2016-05-02 15:01 GMT-06:00 Chang Woon Jang <[email protected]>: > 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? Define "normal". Yes, linear is VOTCA's default. You can change that in potential_extrapolate.sh if you need something different. However, by the end of the day, it doesn't really matter, which interpolation scheme you use as long as it is repulsive enough to pull things back to the mean distance. The original distribution tells you that it is very unlikely to find distances in the extrapolated region anyhow.
Christoph > > > 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. > 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.
