The problem was kind of silly. My settings.xml file had the inappropriate step size for my target bonds. so I changed my settings file to <bonded> <name>bond</name> <min>0.192</min> <max>0.204</max> <step>0.001</step> . . . </bonded> My step was 0.002, instead of 0.001. Once I made that change, the program ran, and I got acceptable results. On Thursday, April 8, 2021 at 12:13:32 PM UTC-4 Christoph Junghans wrote:
> 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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