Dear Christoph Junghans, Can I use csg_inverse for getting bonded and non-bonded potentials instead?
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. 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. 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? 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.
