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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