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!
>>>>> >
>>>>> >
>>>>> > --
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>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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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>
--
Christoph Junghans
Web: http://www.compphys.de
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