2015-10-09 12:33 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear Christoph Junghans, > > Can I use csg_inverse for getting bonded and non-bonded potentials > instead? Yes! Actually csg_inverse does iterative Boltzmann inversion of which calculating potentials is a part of.
> > In the ibi and ibi_bonded of hexane example, it looks like csg_inverse needs > settings.xml if bonded and non-bonded target distributions exist. Yes, you need entries in settings.xml and target distributions for each interaction. > > I ran ./run in the ibi and ibi_bonded directories. Those created series of > step_xxx directories. In those directory of the first iteration (step_001), > for example, xvg files (table_b1.xvg, table_a1.xvg, table_A_A.xvg, > table_A_B.xvg) were generated. The xvg tables in step_001 are the initial guesses out of the target distributions. > > If I am right, those files are potential energies as function of length, or > angle (rad). > > Would you please let me know if I understand the tutorials correctly? Everything correct, see section 7.1 of the manual for details on the iterative workflow! Christoph > > Thank you very much. > > Best regards, > Changwoon Jang > > > On Wed, Oct 7, 2015 at 5:52 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2015-10-07 12:57 GMT-06:00 Chang Woon Jang <[email protected]>: >> > Dear VOTCA users, >> > >> > I am getting used to use VOTCA now. I have a question about tabulated >> > table generated by csg_boltzmann tool. >> > >> > In my system, there are two bead types, A and B. Therefore, I >> > generated >> > A-B-bond.txt using the following command. >> > >> > csg_boltzmann --top topol.tpr --cg TGDDM.xml --trj traj.trr >> > --first-frame >> > 10001 >> > >> > and then, >> > >> > tab A-B-bond.txt *:ABbond:* >> > >> > In my TGDDM.xml file, ABbond defined, >> > >> > <cg_bonded> >> > <bond> >> > <name>ABbond</name> >> > <beads> >> > A1 B1 >> > A2 B1 >> > B2 A3 >> > B2 A4 >> > </beads> >> > </bond> >> > </cg_bonded> >> > >> > >> > Therefor, I got all average ABbond tabulated file called here >> > A-B-bond.txt. >> > There are three columns in this file. I am not sure what those columns >> > are >> > but ... >> > >> > Is this file related to GROMACS input file? >> > >> > Where am I informed of this information for this tabulated potential >> > file >> > format? >> I guess it would work, but most likely you want to post-process the >> potential first, see: >> <https://groups.google.com/d/msg/votca/XdgzvB-Lt8s/9BkBYEKaCAAJ> >> and manual section 4.2 >> >> Christoph >> > >> > Thank you. >> > >> > 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 http://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 http://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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
