I apologize for the incessant questioning... But this is the procedure i have followed: I ran a all-atom simulation on gromacs, obtained all the necessary file (topol.trr, conf.gro, ener.edr, traj.trr). I wrote a mapping file to turn benzene into a two-bead structure. Once I got these files, I ran the following command: csg_boltzmann --top 600-c6h6-MolDynamics.tpr --trj 600-c6h6-MolDynamics.trr --cg benzene.xml < boltzmann_cmds where boltzmann_cmds is:
hist bond.dist.ib *bond* q I got bond.dist.ibi, bond.dist.new from this. I also received A-A.dist.new from: csg_stat --top 600-c6h6-MolDynamics.tpr --trj 600-c6h6-MolDynamics.trr --cg benzene.xml --options settings.xml --nt 6 --begin 200 My bond.dist.new has no u's in the third column. However, it has values only from 0.192 to 0.204 - so a very small range. This is what I am using as my bond.dist.tgt in my IBI. Everything has the "i" flag in the third column. I am getting 3 perl_debug.xxx files in my step_000 folder. The last one had the information I have given in the above message. *As a matter of fact, I ran the same procedure with the hexane file, and it checked out just fine... * I am now wondering if there is something amiss with my settings.xml file, but the errors seem to be pointing squarely at bond.dist.tgt file... Could you explain what I have to do preprocess the data? I did what the page you mentioned asked me to do: csg_resample --in bond.dist.new --out bond.dist.newer --grid 0:0.001:1 I have written out the debug files here: https://justpaste.it/3q0xm Any advice you have would be appreciated!! On Wednesday, April 7, 2021 at 11:41:51 PM UTC-4 Christoph Junghans wrote: > On Wed, Apr 7, 2021 at 20:22 Satyen Dhamankar <[email protected]> wrote: > >> This is also something that I saw... >> 123: die "All data points from file '$infile' are invalid after Boltzmann >> inversion, please check if your distribution is a valid dist.\n" if >> ($valid_i==-1); >> 126: my $first=undef; >> 127: for (my $i=$valid_i;$i>=0;$i--){ >> 128: if ($flag[$i] eq "u") { >> 134: $first=0 unless defined $first; >> 137: my $last=undef; >> 138: for (my $i=$valid_i;$i<=$#pot;$i++){ >> 139: if ($flag[$i] eq "u") { >> 139: if ($flag[$i] eq "u") { >> 139: if ($flag[$i] eq "u") { >> 139: if ($flag[$i] eq "u") { >> 139: if ($flag[$i] eq "u") { >> 139: if ($flag[$i] eq "u") { >> 139: if ($flag[$i] eq "u") { >> 145: $last=$#pot unless defined $last; >> 146: my $n=10; >> 147: my $valid=$last-$first+1; >> 148: die "Only $valid points are valid after Boltzmann inversion from >> file '$infile', please check if your distribution is a valid dist.\n" if >> ($valid < $n); >> >> Does this imply that I have to run post-processing? >> > correct! > > My question is, I see the same zeros in the hexane bond.dist.tgt file, but >> I did not receive an error when I ran that simulation: why is that? >> > you also need to check the flags (3rd column) in the Distribution file as > well , „u“ means undefined, you want an „i“ there for in range. > > Christoph > > On Wednesday, April 7, 2021 at 9:43:17 PM UTC-4 Satyen Dhamankar wrote: >> >>> 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. >> 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/51ef0700-6df2-43d9-8f62-2a5d6f196e76n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/votca/51ef0700-6df2-43d9-8f62-2a5d6f196e76n%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. 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/7dc60b54-2bb5-40a9-ac92-cd7db74696bbn%40googlegroups.com.
