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. 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