On 15 January 2015 at 19:44, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/15/15 11:25 AM, Kalev Takkis wrote: > >> On 15 January 2015 at 00:09, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/14/15 4:44 PM, Kalev Takkis wrote: >>> >>> Hi, list! >>>> >>>> GROMACS complains about inconsistent shifts and suggests me to check my >>>> topology. I have so done, but the problem is not immediately obvious. >>>> How >>>> can I make it tell me exactly which atoms/bonds it finds faulty? >>>> >>>> >>>> What were you doing when the error came up? What was your exact >>> command? >>> What is your system? >>> >>> >> Temperature equilibration, commands given were >> gmx grompp -f nvt.mdp -c simcell_minim.gro -p simcell.top -o >> simcell_temp.tpr >> gmx mdrun -v -deffnm simcell_temp >> >> GROMACS version 5.0.4, ff OPLS-AA >> Equilibration finishes without other problems, I can continue with the >> next >> step without the system blowing up. The error is not encountered during >> minimisation, it finishes fine, energies are reasonable and no trace of >> inconsistent shifts is found in the log. >> System is chromatography column, silica slab with attached hydrocarbon >> chains. The crystal surface is infinite in xz plane, so the mdp file >> specifies >> pbc = xyz >> periodic_molecules = yes >> >> > Have you verified that all the bonded terms that span a periodic boundary > are specified correctly? > > The model is hacked together from silica unit cell and chains using >> pdb2gmx, so it's entirely possible that there is indeed something wrong >> with my system. I'd like to know where. When GROMACS encounters this error >> > > The topology is the first and most likely source of error. > > can I make it reveal more details? Which atoms/bonds are involved? Some >> diagnostics tool or verbosity switch to mdrun maybe? >> >> > How soon does the system blow up? General troubleshooting advice is at > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_ > Unstable_System >
It doesn't. Noticed the message in the terminal window when I was trying to improve the visual with trjconv after the production run. Then went back through the logs and found that it was first reported in NVE equilibration. > > All GROMACS tools have a -debug flag that can be set, but you'll dump out > a massive file with a ton of information you don't need. If you're not > used to reading through it, it can be more of an obstacle than a useful > tool :) No kidding. 1 step run -> 25MB log file. Fortunately grep was able to extract the list of wonky atoms in a nice concise manner. Thank you for the advice. All the best, Kalev > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
