2016-08-29 15:19 GMT-06:00 Chang Woon Jang <[email protected]>: > 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. Please send me the table and the xml off-list and I will have a look.
And of course you can run IBI on a subset of the interactions, see <https://github.com/votca/csg-tutorials/tree/master/hexane/ibi> In this example only the non-bonded interactions are iterated. Christoph > > 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. -- 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.
