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? 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.
<cg> <!-- example for a non-bonded interaction entry --> <non-bonded> <!-- name of the interaction --> <name>A-A</name> <!-- types involved in this interaction --> <type1>A</type1> <type2>A</type2> <!-- dimension + grid spacing of tables for calculations --> <min>0</min> <max>1.5</max> <step>0.01</step> <inverse> <target>A-A.dist.tgt</target> <do_potential>1 0 0</do_potential> <post_update></post_update> <post_add>convergence</post_add> <gromacs> <table>table_A_A.xvg</table> </gromacs> </inverse> </non-bonded> <inverse> <kBT>2.47772</kBT> <program>gromacs</program> <gromacs> <equi_time>20</equi_time> <table_bins>0.002</table_bins> <pot_max>1000000</pot_max> <table_end>5.0</table_end> <mdrun> <opts>-nt 6</opts> </mdrun> </gromacs> <filelist>grompp.mdp topol.top table.xvg table_a1.xvg table_b1.xvg index.ndx</filelist> <iterations_max>5</iterations_max> <convergence_check> <type>default</type> <limit>0.001</limit> </convergence_check> <method>ibi</method> <log_file>inverse.log</log_file> <restart_file>restart_points.log</restart_file> </inverse> </cg>
