On Thu, Apr 8, 2021 at 9:43 AM Satyen Dhamankar <[email protected]> wrote: > > Thank you Christoph, I have figured out the problem! Nice. Could you please post your solution here for others to learn?
Thanks, Christoph > Sincerely, > Satyen Dhamankar > > > On Thu, Apr 8, 2021 at 9:54 AM Christoph Junghans <[email protected]> wrote: >> >> >> >> On Thu, Apr 8, 2021 at 07:52 Christoph Junghans <[email protected]> wrote: >>> >>> 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. >> >> Also make sure the range in your settings.xml is the same. >>> >>> >>> > 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 >> >> -- >> 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/CAHG27e5dHtWcyVi%3DLm59UaRHkAhTvnC1yA17TQcRicmdj08HXA%40mail.gmail.com. > > -- > 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/CAFMHqF9wbuaz-SJWNgnG8NgmPdput4LuKEv_7QttHU_kEqVO-g%40mail.gmail.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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