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?
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? 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.
