2016-01-26 12:08 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Votca Users, > > > I have a simple question. I have run IBI for my own polymer system using > csg_inverse --option setting.xml following votca tutorials. > > When I first ran IBI in my desktop, the iterations stopped at Step 5 with > the following error. > ------------------------------------------------------- > Program gmx, VERSION 5.0.8-dev-20151014-1f04b58 > Source code file: > /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec_top.c, line: > 394 > > Fatal error: > 2 of the 900 bonded interactions could not be calculated because some atoms > involved moved further apart than the multi-body cut-off distance (1.5 nm) > or the two-body cut-off distance (1.5 nm), see option -rdd, for pairs and > tabulated bonds also see option -ddcheck > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > Then, I re-ran the same IBI without changing anything in setting.xml and > grompp.mdp files. It stopped 16 Step (Step 16) with error "1 of the 900 > bonded ...". Is there a reason for this? Usually that means one of the tables is screwed up. Go in step_016 or step_005 and have a look at table.*xvg (column 1 vs column 6).
Maybe you have to pick min and max differently or run longer per step for better statistics. 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 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.
