Dear Christoph, Can I run ibi without dihedrals? Actually, I do not need dihedral potentials even though CG molecules have dihedrals. Or, any suggestions for debugging the dihedrals. Actually, the warning signs disappeared but I have still the same Fatal error.
Thank you. Best regards, Changwoon Jang On Mon, Aug 29, 2016 at 4:30 PM, Christoph Junghans <[email protected]> wrote: > 2016-08-29 13:32 GMT-06:00 Chang Woon Jang <[email protected]>: > > Dear Votca Users, > > > > I have four dihedral distributions directly from csg_boltzmann. > However, > > only one dihedral distribution gives waning sign during IBI run as > follows. > > > > WARNING: For the 359 non-zero entries for table 0 in table_d1.xvg the > forces > > deviate on average 196% from minus the numerical derivative of the > potential > That means something went wrong in the table conversion! > > > > > > > > Then, the IBI fails with Fatal error: 1 of the 1720 bonded interactions > > could not be calculated because some atoms involved moved further apart > than > > the multi-body cut-off distance (2.02391 nm) or the two-body cut-off > > distance (2.02391 nm), see option -rdd, for pairs and tabulated bonds > also > > see option -ddcheck > That is most likely due to the above warning. > > > > > > I am not sure why only one dihedral gives this warning and prevent IBI > run. > > Do you have any comments on that? > IBI for dihedral interactions is a bit tricky and not very well > testing in VOTCA, so you will need to do a bit a debugging on your > side. > > Christoph > > > > > I have converted dihedral distribution radian to angle (only first > column) > > due to the ibi requirement just using unit convert x*180/3.14 (x is > > radian). > > > > 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 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.
