2016-01-26 13:31 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > What does table.*xvg give me a sign for screwing up? > > In the setting file, I have set min and max, 0 and 1.5 for all interactions > except for one A-D interaction. > > I took a look at table*.xvg files in step016 (1 vs 6 columns), but nothing > strange. I drew all interactions and those looked fine. > > I also increased iterations_max to 1000. But the same error at step004 (2 of > the 900 bonded interactions could not be calculated because some atoms) > still came out. > > > Would picking different min and max help solve this error? Looking at the table just helps to see if the potential are sane, sometimes VOTCA get extrapolation wrong. Non-bonded interactions should have a modified L shape (coming from inf for small r and go to 0 for big r), bonded potentials should look like a modified U (coming from inf for small r and go to inf for big r) and so one.
The error get is a Gromacs errer, which usually means some bonded interactions could not be calculated because atoms got to far apart, which usually means your system exploded. Christoph > > Thank you. > > Best regards, > Changwoon Jang > > > > > > On Tue, Jan 26, 2016 at 2:31 PM, Christoph Junghans <[email protected]> > wrote: >> >> 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. > > > > > -- > 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.
