Hello, The simulation I am running is of a molecule comprising of two identical beads held together by a bond. I ran the following on my coarse-grained simulation:
csg_inverse --options settings.xml --debug I have been working on this, and I have been receiving this message: Appending to existing logfile inverse.log We are doing Method: ibi Prepare (dir step_000) Using initial guess from dist bond.dist.tgt for bond ############################################################################################################################################# # # # ERROR: # # do_external: subscript # # /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/dist_boltzmann_invert.pl --type bond --kbT 2.47772 --min 1e-10 bond.dist.tgt bond.pot.new.raw.cQ7 # # (from tags dist invert) failed # # For details see the logfile /tigress/satyend/benzene_simulations/opls-aa/r_cutoff-1.5-org/VOTCA/TwoBead_CG/ibi/inverse.log # ############################################################################################################################################## Terminated What could the cause of such an error message be? On Tuesday, April 6, 2021 at 8:20:11 AM UTC-4 Christoph Junghans wrote: > > > On Mon, Apr 5, 2021 at 22:56 Satyen Dhamankar <[email protected]> wrote: > >> Thank you for your advice, Christoph. >> >> How do you recommend I use harmonic potentials for a CG simulation? I >> have the bond.dist.new histogram after I did my mapping, I can use the >> modal bond length I obtained from that. However, what can I use as my >> spring constant? >> > you can do a boltzmann inversion and then do a quadratic fit. > >> >> Using csg_boltzmann on my bond distribution, I obtained the table at 298 >> K and set bond, however, the table that was created started at 0.19 nm. My >> question is, when performing a boltzmann inversion on the bond >> distribution, how do we treat the bins with a height of 0? should the >> number at that point simply be inf? >> > You will have to do a little bit of post-processing: > https://www.votca.org/csg/preparing.html#post-processing-of-the-potential > >> > >> >> This is my mapping file, just to be complete: >> <cg_molecule> >> <name>BNZ</name> <!-- the name of the molecule after mapping--> >> <ident>UNK</ident> <!-- name of the actual atom --> >> <topology> >> <cg_beads> >> <cg_bead> >> <name>B1</name> >> <type>CG</type> >> <symmetry>1</symmetry> >> <mapping>A</mapping> >> <beads> >> 1:UNK:C00 1:UNK:C01 1:UNK:C02 1:UNK:H06 1:UNK:H07 1:UNK:H08 >> </beads> >> </cg_bead> >> >> <cg_bead> >> <name>B2</name> >> <type>CG</type> >> <symmetry>1</symmetry> >> <mapping>A</mapping> >> <beads> >> 1:UNK:C03 1:UNK:C04 1:UNK:C05 1:UNK:H09 1:UNK:H0A 1:UNK:H0B >> </beads> >> </cg_bead> >> </cg_beads> >> >> <cg_bonded> >> <bond> >> <name>bond</name> >> <beads> >> B1 B2 >> </beads> >> </bond> >> </cg_bonded> >> </topology> >> >> <maps> >> <map> >> <name>A</name> >> <weights>12.0110 12.0110 12.0110 1.0080 1.0080 1.0080</weights> >> </map> >> </maps> >> </cg_molecule> >> >> I used this file as my mapping file when I executed: >> csg_boltzmann --top topol.tpr --trj trajectory.trj --cg bezene.xml >> tab set T 298 >> tab set scale bond >> tab table_b1.xvg *:bond:* >> On Monday, April 5, 2021 at 9:09:15 PM UTC-4 Christoph Junghans wrote: >> >>> On Mon, Apr 5, 2021 at 2:20 PM Satyen Dhamankar <[email protected]> >>> wrote: >>> > >>> > Hello, >>> > >>> > I am performing a coarse-grained simulation of benzene, where I am >>> converting C6H6 into two beads. Where each bead is essentially C3H3, and >>> they are connected by a bond. >>> > >>> > I want to perform IBI on this coarse-grained simulation using votca >>> and gmx, but I am having some problems. >>> > >>> > The command I am running is: >>> > csg_inverse --options settings.xml >>> > >>> > I am getting an energy divergence (blows up to infinity) when votca >>> runs mdrun. This is the error I see in my inverse.log file: >>> > >>> > Program: gmx mdrun, version 2019.6 >>> > Source file: src/gromacs/mdlib/sim_util.cpp (line 752) >>> > MPI rank: 1 (out of 6) >>> > Fatal error: >>> > Step 0: The total potential energy is inf, which is not finite. The LJ >>> and >>> > electrostatic contributions to the energy are inf and 0, respectively. >>> A >>> > non-finite potential energy can be caused by overlapping interactions >>> in >>> > bonded interactions or very large or Nan coordinate values. Usually >>> this is >>> > caused by a badly- or non-equilibrated initial configuration, >>> incorrect >>> > interactions or parameters in the topology. >>> > For more information and tips for troubleshooting, please check the >>> GROMACS >>> > website at http://www.gromacs.org/Documentation/Errors >>> > >>> > I am running a minimization script, but I don't see why energy is >>> blowing up. >>> > >>> > I also am unsure of what the table_b1.xvg and table_a1.xvg files are >>> for. I naively got these files from the hexane tutorial. What are these >>> files for? How do I make them? >>> These two tables are for the bonded interactions, they are just >>> boltzmann-inverted tables from the bonded distributions (do that by >>> hand or use csg_boltzmann). >>> You could also use harmonic potentials as a start to make your life >>> easier. >>> >>> Christoph >>> > >>> > I have attached my grommp.mdp, conf.gro, settings.xml, topol.top and >>> tables files. >>> > >>> > Any advice you have would be appreciated! >>> > >>> > >>> > -- >>> > Join us on Slack: https://join.slack.com/t/votca/signup >>> > --- >>> > 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 view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/956dbed6-f6a1-4269-866c-a4a8c5a6428cn%40googlegroups.com. >>> >>> >>> >>> >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >>> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/5b85becb-b3ce-414e-8409-d6f2399e7a81n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/votca/5b85becb-b3ce-414e-8409-d6f2399e7a81n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- > Christoph Junghans > Web: http://www.compphys.de > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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