On Wed, Apr 7, 2021 at 11:23 PM Satyen Dhamankar <[email protected]> wrote: > > 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!! Ok the perl files aren't super useful for find issue in the input files, they are more for then you need to add a script to VOTCA. Here is what I would try; - also make - look at inverse.log, above the big error banner there is usually an error message from the script - try to run the script that fails by hand, in your case, tags were "dist invert", so try $ csg_call --options settings.xml --ia-name bond --ia-type bond dist invert --type bond --kbT 2.47772 --min 1e-10 bond.dist.tgt bond.pot.new.raw.cQ7 - look at the input file (you already did that), e.g. bond.dist.tgt to see if the range is right.
> > 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. >>>>> >>>>> -- >>>>> 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. >> >> -- >> 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. -- 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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