Thank you Christoph, I have figured out the problem! 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 > <https://groups.google.com/d/msgid/votca/CAHG27e5dHtWcyVi%3DLm59UaRHkAhTvnC1yA17TQcRicmdj08HXA%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- 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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