On Thu, Apr 8, 2021 at 7:02 PM Satyen Dhamankar <[email protected]> wrote: > > 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>
Ah ok, thanks for letting us know. Christoph > 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. > 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/82e3b11c-756b-43c1-820b-20e14b2257fan%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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