Hi Christoph,
I have corrected the mapping file. However, when creating the exclusion.txt
I noticed this file was not correct. For this I generated a .tpr file
without exclusions
and use:
csg_boltzmann --top mma_trimer_sd_noexclusions.tpr --cg
mma_trimer_mapping.xml --excl exclusions.txt
I used votca 1.6.2. I tried two other versions of votca, sourcing someone
else installation, votca 1.6-dev and a local machine version.
I supposed this is a problem with my installation. Is there a way to check
that votca was installed correctly? I did not get any error while
installing it. And I have not seen anyone with this problem browsing the
messages.
I have attached the mapping file and the exclusion files for the different
votca versions.
details of the versions below
csg_boltzmann, version 1.6.2 gitid: 9b6bbd0 (compiled Dec 19 2020, 15:56:40)
votca_tools, version 1.6.2 gitid: 9b6bbd0 (compiled Dec 19 2020, 15:55:42)
gromacs, 2019.4 (single precision)
csg_boltzmann, version 1.6-dev gitid: e42c3e100 (compiled Jun 30 2020,
17:41:20)
votca_tools, version 1.6-dev gitid: e42c3e100 (compiled Jun 30 2020,
17:40:52)
gromacs, 2019.4 (single precision)
csg_boltzmann, version 1.5 (compiled Feb 8 2019, 02:59:36)
votca_tools, version 1.5 (compiled Feb 8 2019, 02:57:53)
gromacs, 2019.1 (double precision)
On Sunday, 27 December 2020 at 10:18:45 UTC+1 nancyfor wrote:
> Thanks Christoph, I completely overlooked this.
> Cheers,
> Nancy
>
> On Sunday, 27 December 2020 at 01:23:11 UTC+1 Christoph Junghans wrote:
>
>> On Sat, Dec 26, 2020 at 4:29 PM nancyfor <[email protected]> wrote:
>> >
>> > Hello everybody,
>> >
>> > I am trying to get the probability distribution functions and the
>> tabulated potentials for a system with 11 coarse grained beads. However
>> when listing all available bonded interaction only list 3. Coincidentally,
>> they are the last bonded interactions for angle, bond and dihedral sections
>> respectively. I am using votca 1.6.2 and gromacs 2019.4
>> >
>> > This is the output for
>> >
>> > csg_boltzmann --top topol.tpr --trj traj.xtc --cg mapping.xml
>> > list
>> >
>> > Available bonded interactions:
>> > molecule 0:EMBT:index 0
>> > molecule 0:MBT:index 0
>> > molecule 0:SMEMBT:index 0
>> >
>> > I have checked if the mapping was correct using csg_dump, and it seems
>> is fine.
>> >
>> > I have attached the mapping file in case you spot any mistake.
>> Yeah, you need to put each bond, angle, dihedral in its own <bond>,
>> <angle>, <dihedral> block, otherwise all properties (name, beads etc)
>> will be overwritten by the latest entry and hence you end up with one
>> of each.
>>
>> If the documentation is unclear on that, please modify the
>> input_files.rst file in the share/doc folder of the csg module and
>> send up as a patch or submit a pull request on GitHub.
>>
>> Christoph
>>
>> > Best regards,
>> > Nancy
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> > ---
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>> .
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>
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<cg_molecule>
<name>MMA3</name>
<ident>3-MMA</ident>
<topology>
<cg_beads>
<cg_bead>
<name>H</name>
<type>H</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>H</mapping>
<beads>1:HMA:C7 1:HMA:H12 1:HMA:H13 1:HMA:H14 </beads>
</cg_bead>
<cg_bead>
<name>1MB</name>
<type>MB</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>MB</mapping>
<beads>1:HMA:C3 1:HMA:C2 1:HMA:H4 1:HMA:H5 1:HMA:C4 1:HMA:H6 1:HMA:H7 1:HMA:H8 </beads>
</cg_bead>
<cg_bead>
<name>1E</name>
<type>E</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>E</mapping>
<beads>1:HMA:C5 1:HMA:O1 1:HMA:O2 </beads>
</cg_bead>
<cg_bead>
<name>1SM</name>
<type>SM</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>SM</mapping>
<beads>1:HMA:C6 1:HMA:H9 1:HMA:H10 1:HMA:H11 </beads>
</cg_bead>
<cg_bead>
<name>2MB</name>
<type>MB</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>MB</mapping>
<beads>2:MMA:C3 2:MMA:C2 2:MMA:H4 2:MMA:H5 2:MMA:C4 2:MMA:H6 2:MMA:H7 2:MMA:H8 </beads>
</cg_bead>
<cg_bead>
<name>2E</name>
<type>E</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>E</mapping>
<beads>2:MMA:C5 2:MMA:O1 2:MMA:O2 </beads>
</cg_bead>
<cg_bead>
<name>2SM</name>
<type>SM</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>SM</mapping>
<beads>2:MMA:C6 2:MMA:H9 2:MMA:H10 2:MMA:H11 </beads>
</cg_bead>
<cg_bead>
<name>3MB</name>
<type>MB</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>MB</mapping>
<beads>3:TMA:C3 3:TMA:C2 3:TMA:H4 3:TMA:H5 3:TMA:C4 3:TMA:H6 3:TMA:H7 3:TMA:H8 </beads>
</cg_bead>
<cg_bead>
<name>3E</name>
<type>E</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>E</mapping>
<beads>3:TMA:C5 3:TMA:O1 3:TMA:O2 </beads>
</cg_bead>
<cg_bead>
<name>3SM</name>
<type>SM</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>SM</mapping>
<beads>3:TMA:C6 3:TMA:H9 3:TMA:H10 3:TMA:H11 </beads>
</cg_bead>
<cg_bead>
<name>T</name>
<type>T</type>
<symmetry>1</symmetry> <!-- defines the type of cg bead -->
<mapping>T</mapping>
<beads>3:TMA:C1 3:TMA:H1 3:TMA:H2 3:TMA:H3 </beads>
</cg_bead>
</cg_beads>
<cg_bonded><!-- bonded interactions -->
<bond>
<name>HMB</name>
<beads>
H 1MB
</beads>
</bond>
<bond>
<name>MBE</name>
<beads>
1MB 1E
2MB 2E
3MB 3E
</beads>
</bond>
<bond>
<name>MBMB</name>
<beads>
1MB 2MB
2MB 3MB
</beads>
</bond>
<bond>
<name>ESM</name>
<beads>
1E 1SM
2E 2SM
3E 3SM
</beads>
</bond>
<bond>
<name>MBT</name>
<beads>
3MB T
</beads>
</bond>
<angle>
<name>HMBE</name>
<beads>
H 1MB 1E
</beads>
</angle>
<angle>
<name>HMBMB</name>
<beads>
H 1MB 2MB
</beads>
</angle>
<angle>
<name>MBESM</name>
<beads>
1MB 1E 1SM
2MB 2E 2SM
3MB 3E 3SM
</beads>
</angle>
<angle>
<name>MBMBMB</name>
<beads>
1MB 2MB 3MB
</beads>
</angle>
<angle>
<name>MBMBE</name>
<beads>
1MB 2MB 2E
2MB 3MB 3E
2MB 1MB 1E
3MB 2MB 2E
</beads>
</angle>
<angle>
<name>MBMBT</name>
<beads>
2MB 3MB T
</beads>
</angle>
<angle>
<name>EMBT</name>
<beads>
3E 3MB T
</beads>
</angle>
<dihedral>
<name>HMBESM</name>
<beads>
H 1MB 1E 1SM
</beads>
</dihedral>
<dihedral>
<name>HMBMBMB</name>
<beads>
H 1MB 2MB 3MB
</beads>
</dihedral>
<dihedral>
<name>HMBMBE</name>
<beads>
H 1MB 2MB 2E
</beads>
</dihedral>
<dihedral>
<name>MBMBESM</name>
<beads>
1MB 2MB 2E 2SM
2MB 3MB 3E 3SM
3MB 2MB 2E 2SM
2MB 1MB 1E 1SM
</beads>
</dihedral>
<dihedral>
<name>EMBMBE</name>
<beads>
1E 1MB 2MB 2E
2E 2MB 3MB 3E
</beads>
</dihedral>
<dihedral>
<name>MBMBMBE</name>
<beads>
1MB 2MB 3MB 3E
3MB 2MB 1MB 1E
</beads>
</dihedral>
<dihedral>
<name>MBMBMBT</name>
<beads>
1MB 2MB 3MB T
</beads>
</dihedral>
<dihedral>
<name>EMBMBT</name>
<beads>
2E 2MB 3MB T
</beads>
</dihedral>
<dihedral>
<name>SMEMBT</name>
<beads>
3SM 3E 3MB T
</beads>
</dihedral>
</cg_bonded>
</topology>
<maps>
<map>
<name>H</name>
<weights> 12.011 1.008 1.008 1.008</weights>
</map>
<map>
<name>MB</name>
<weights> 12.011 12.011 1.008 1.008 12.011 1.008 1.008 1.008</weights>
</map>
<map>
<name>E</name>
<weights> 12.011 15.999 15.999</weights>
</map>
<map>
<name>SM</name>
<weights> 12.011 1.008 1.008 1.008</weights>
</map>
<map>
<name>T</name>
<weights> 12.011 1.008 1.008 1.008</weights>
</map>
</maps>
</cg_molecule>
# atomistic: 3-MMA cg: 3-MMA cgmap: mma_trimer_mapping.xml
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