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? 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?
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
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>>>>
>>> > 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
>>>>
>>> --
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>>>
>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/votca/5b85becb-b3ce-414e-8409-d6f2399e7a81n%40googlegroups.com
>>>
>>> <https://groups.google.com/d/msgid/votca/5b85becb-b3ce-414e-8409-d6f2399e7a81n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>
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