Hi Christoph,
I followed your suggestion, but again i am getting the following error:
ERROR:
#
# potential_to_lammps.sh: cg.inverse.program was not set to 'lammps', but
'gromacs' (mind the default) #
# Details can be found above
The bond.xml script which i am using is shown below:
<cg>
<bonded>
<!-- name of the interaction -->
<name>bond-AB</name>
<min>0.20</min>
<max>0.361</max>
<step>0.001</step>
<inverse>
<program>lammps</program>
<!--<lammps>-->
<!-- name of the table for lammps run -->
<table>CG-BOND-AB.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.20</table_begin>
<table_end>0.361</table_end>
<table_bins>0.001</table_bins>
<!--</lammps>-->
</inverse>
</bonded>
</cg>
And i am using the following command:
csg_call --ia-type bond --ia-name bond-AB --options bond.xml
convert_potential lammps --clean input_bond-AB.pot table_AB.xvg
Just to keep you updated, i wish to get the bonded potential using
boltzmann inversion. I am using the following command to get the bonded
distribution:
csg_boltzmann --top topology.xml --trj Trajectory2.dump --cg PEO-10.xml <
boltzmann_cmds
Then, i am using the following command to get the bonded potential:
csg_boltzmann --top topology.xml --trj Trajectory2.dump --cg PEO-10.xml <
boltzmann_cmds
Then, i am using the following command for smoothening of the potentials:
csg_call --sloppy-tables table smooth bond.pot.ib input_bond.pot
And finally, the following command to convert the bonded potential to
LAMMPS tables form. It is at this point where I am getting the error.
csg_call --ia-type bond --ia-name bond-AB --options bond.xml
convert_potential lammps --clean input_bond-AB.pot table_AB.xvg
Also, can you please explain this part: "Also if you set
table_begin, table_bins and table_end to the same values as min, step and
max respectively, it is kind of pointless to set them". I mean the
difference between min and table_begin, max and table_end.
Sorry, for my ignorance and long post.
Thank you.
Sanjeet
On Saturday, September 10, 2022 at 9:39:40 PM UTC-4 Christoph Junghans
wrote:
> On Sat, Sep 10, 2022 at 10:23 AM Sanjeet Singh <[email protected]> wrote:
>
>> Hi,
>>
>> Can you please check my bond.xml file? if everything is correct there.
>>
> Sorry the entry VOTCA is looking for inverse.lammps.table_bins, and you
> (and I in my example) missed the <inverse> indentation of the block, try:
> <bond>
> <name>foo</name>
> <inverse>
> <lammps>
> <table_bins>0.01</table_bins>
> </lammps>
> </inverse>
> </bond>
>
> Also if you set table_begin, table_bins and table_end to the same
> values as min, step and max respectively, it is kind of pointless to set
> them.
>
> Christoph
>
>>
>> On Saturday, September 10, 2022 at 12:13:56 PM UTC-4 Sanjeet Singh wrote:
>>
>>> Hi Christoph,
>>>
>>> I have moved my <lammps> block inside the <bond> block. But again, i am
>>> getting the following error.
>>>
>>> ERROR:
>>>
>>> #
>>> # csg_get_interaction_property: Could not get 'max' for interaction with
>>> name 'bond-AB' from bond.xml and no default was found in
>>> /usr/share/votca/xml/csg_defaults.xml #
>>> # Details can be found above
>>>
>>> And, if i am setting the min, max, and step value, as shown in my
>>> bond.xml file, THEN the <lammps> block is not read again, and i am getting
>>> the following error.
>>>
>>> ERROR:
>>>
>>> #
>>> # do_external: subscript
>>>
>>> #
>>> # /usr/share/votca/scripts/inverse/table_to_tab.pl --header lammps
>>> --type bond input_bond-AB.pot.shift.dq5Vy input_bond-AB.pot.deriv.JWRcY
>>> ./table/table_AB.xvg #
>>> # (from tags convert_potential tab) failed
>>>
>>> #
>>> # Details can be found above
>>>
>>> I am attaching all my files here for your reference.
>>> On Friday, September 9, 2022 at 10:42:55 PM UTC-4 Christoph Junghans
>>> wrote:
>>>
>>>> On Fri, Sep 9, 2022 at 7:01 PM Sanjeet Singh <[email protected]>
>>>> wrote:
>>>>
>>>>> Hi Christoph,
>>>>>
>>>>> Thank you for your prompt response. Actually, i am not able to
>>>>> understand the following lines:
>>>>>
>>>>> csg_get_interaction_property: No value for 'inverse.lammps.table_bins'
>>>>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>>>> csg_get_interaction_property: returning emtpy value for
>>>>> 'inverse.lammps.table_bins'
>>>>> csg_get_interaction_property: No value for
>>>>> 'inverse.lammps.table_begin' found in bond.xml, trying
>>>>> /usr/share/votca/xml/csg_defaults.xml
>>>>> csg_get_interaction_property: returning emtpy value for
>>>>> 'inverse.lammps.table_begin'
>>>>>
>>>>
>>>>
>>>>>
>>>>> I have given the values of table_bins, table_begin, in my bond.xml
>>>>> file. But, i don't think csg_call is reading these values from there. And
>>>>> same is the case for lammps.scale and lammps.y_scale. Why csg_call is
>>>>> taking the default values, if the values for these parameters are already
>>>>> given in bond.xml file.
>>>>>
>>>>
>>>> The table properties etc are an per-interaction property (hence the
>>>> line with csg_get_interaction_property instead of csg_get_property)
>>>> So for VOTCA to read it you will have to move that part of the <lammps>
>>>> block inside the <bond> block, e.g.
>>>> <bond>
>>>> <name>foo</name>
>>>> <lammps>
>>>> <table_bins>0.01</table_bins>
>>>> </lammps>
>>>> </bond>
>>>>
>>>>
>>>>
>>>>>
>>>>> And furthermore, what is the meaning of scriptpath in the following
>>>>> lines.
>>>>>
>>>>> csg_get_property: No value for 'cg.inverse.scriptpath' found in
>>>>> bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>>>> csg_get_property: returning emtpy value for 'cg.inverse.scriptpath'
>>>>>
>>>> VOTCA has the option to use user-provided scripts, e.g. you can use
>>>> your own custom interpolation script, and the script path would be the
>>>> place where you would put them.
>>>> For standard usage, this is ok to be empty.
>>>>
>>>> Christoph
>>>>
>>>>>
>>>>> Thank you.
>>>>>
>>>>> Sanjeet
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Sep 9, 2022 at 6:34 PM Christoph Junghans <[email protected]>
>>>>> wrote:
>>>>>
>>>>>> On Fri, Sep 9, 2022 at 1:06 PM Sanjeet Singh <[email protected]>
>>>>>> wrote:
>>>>>> >
>>>>>> > Hi Christoph,
>>>>>> >
>>>>>> > I am trying to convert the bonded potential to LAMMPS table. For
>>>>>> this, i am using the following command:
>>>>>> >
>>>>>> > csg_call --ia-type bond --ia-name bond-AB --options bond.xml
>>>>>> convert_potential lammps --clean input_bond-AB.pot table_AB.xvg
>>>>>> >
>>>>>> > I am able to get the final output file table_AB.xvg.
>>>>>> >
>>>>>> > But, i am not able to understand the following lines on TERMINAL.
>>>>>> >
>>>>>> > csg_get_property: No value for 'cg.inverse.scriptpath' found in
>>>>>> bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>>>>> > csg_get_property: returning emtpy value for 'cg.inverse.scriptpath'
>>>>>> > We are using Sim Program: lammps
>>>>>> > Running subscript 'potential_to_lammps.sh --clean input_bond-AB.pot
>>>>>> ./TABLE/table_AB.xvg' (from tags convert_potential lammps) dir
>>>>>> /usr/share/votca/scripts/inverse
>>>>>> > Convert input_bond-AB.pot to ./TABLE/table_AB.xvg
>>>>>> > csg_get_interaction_property: No value for
>>>>>> 'inverse.lammps.table_bins' found in bond.xml, trying
>>>>>> /usr/share/votca/xml/csg_defaults.xml
>>>>>> > csg_get_interaction_property: returning emtpy value for
>>>>>> 'inverse.lammps.table_bins'
>>>>>> > csg_get_interaction_property: No value for
>>>>>> 'inverse.lammps.table_begin' found in bond.xml, trying
>>>>>> /usr/share/votca/xml/csg_defaults.xml
>>>>>> > csg_get_interaction_property: returning emtpy value for
>>>>>> 'inverse.lammps.table_begin'
>>>>>> > csg_get_interaction_property: No value for
>>>>>> 'inverse.lammps.table_end' found in bond.xml, trying
>>>>>> /usr/share/votca/xml/csg_defaults.xml
>>>>>> > csg_get_interaction_property: returning emtpy value for
>>>>>> 'inverse.lammps.table_end'
>>>>>> > csg_get_interaction_property: No value for 'inverse.lammps.scale'
>>>>>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>>>>> > csg_get_interaction_property: value for 'inverse.lammps.scale' from
>>>>>> /usr/share/votca/xml/csg_defaults.xml: 1
>>>>>> > csg_get_interaction_property: No value for 'inverse.lammps.y_scale'
>>>>>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>>>>> > csg_get_interaction_property: value for 'inverse.lammps.y_scale'
>>>>>> from /usr/share/votca/xml/csg_defaults.xml: 1
>>>>>> > Running critical command 'mktemp input_bond-AB.pot.smooth.XXXXX'
>>>>>> > Running critical command 'csg_resample --in input_bond-AB.pot --out
>>>>>> input_bond-AB.pot.smooth.I7rqa --grid 0:0.001:1.0'
>>>>>> > Running critical command 'mktemp input_bond-AB.pot.extrapol.XXXXX'
>>>>>> > csg_get_interaction_property: No value for
>>>>>> 'inverse.lammps.table_left_extrapolation' found in bond.xml, trying
>>>>>> /usr/share/votca/xml/csg_defaults.xml
>>>>>> > csg_get_interaction_property: returning emtpy value for
>>>>>> 'inverse.lammps.table_left_extrapolation'
>>>>>> > csg_get_interaction_property: No value for
>>>>>> 'inverse.lammps.table_right_extrapolation' found in bond.xml, trying
>>>>>> /usr/share/votca/xml/csg_defaults.xml
>>>>>> > csg_get_interaction_property: returning emtpy value for
>>>>>> 'inverse.lammps.table_right_extrapolation'
>>>>>> > Running subscript 'potential_extrapolate.sh --clean --type bond
>>>>>> input_bond-AB.pot.smooth.I7rqa input_bond-AB.pot.extrapol.IjNh9' (from
>>>>>> tags
>>>>>> potential extrapolate) dir /usr/share/votca/scripts/inverse
>>>>>> > Extrapolate input_bond-AB.pot.smooth.I7rqa to
>>>>>> input_bond-AB.pot.extrapol.IjNh9
>>>>>> > Running critical command 'mktemp
>>>>>> input_bond-AB.pot.smooth.I7rqa.onlyleft.XXXXX'
>>>>>> > Running subscript 'table_extrapolate.pl --function linear
>>>>>> --avgpoints 3 --region left input_bond-AB.pot.smooth.I7rqa
>>>>>> input_bond-AB.pot.smooth.I7rqa.onlyleft.FDhHj' (from tags table
>>>>>> extrapolate) dir /usr/share/votca/scripts/inverse
>>>>>> > table_extrapolate.pl: extrapolating the left using linear with
>>>>>> gradient -2509.86163466666
>>>>>> > Running subscript 'table_extrapolate.pl --function linear
>>>>>> --avgpoints 3 --region right
>>>>>> input_bond-AB.pot.smooth.I7rqa.onlyleft.FDhHj
>>>>>> input_bond-AB.pot.extrapol.IjNh9' (from tags table extrapolate) dir
>>>>>> /usr/share/votca/scripts/inverse
>>>>>> > table_extrapolate.pl: extrapolating the right using linear with
>>>>>> gradient 2241.54540033333
>>>>>> > Running critical command 'mktemp input_bond-AB.pot.interpol.XXXXX'
>>>>>> > Running critical command 'mktemp input_bond-AB.pot.deriv.XXXXX'
>>>>>> > Running critical command 'csg_resample --in
>>>>>> input_bond-AB.pot.extrapol.IjNh9 --out input_bond-AB.pot.interpol.LyEum
>>>>>> --grid 0:0.001:1.0 --der input_bond-AB.pot.deriv.TAbSL --comment Created
>>>>>> on
>>>>>> Fri Sep 9 03:02:09 PM EDT 2022 by sanjeetsingh@fedora
>>>>>> > called from potential_to_lammps.sh, version 2022-dev
>>>>>> > settings file:
>>>>>> '/home/sanjeetsingh/Documents/SANJEET-PEO/PEO-TRIAL/MAPPING-TRIAL/RDF-GENERATION/BONDED-POTENTIAL/bond.xml'
>>>>>> > working directory:
>>>>>> /home/sanjeetsingh/Documents/SANJEET-PEO/PEO-TRIAL/MAPPING-TRIAL/RDF-GENERATION/BONDED-POTENTIAL'
>>>>>> > Running critical command 'mktemp input_bond-AB.pot.shift.XXXXX'
>>>>>> > Running subscript 'potential_shift.pl --type bond
>>>>>> input_bond-AB.pot.interpol.LyEum input_bond-AB.pot.shift.moz4C' (from
>>>>>> tags
>>>>>> potential shift) dir /usr/share/votca/scripts/inverse
>>>>>> > Running subscript 'table_to_tab.pl --header lammps --type bond
>>>>>> input_bond-AB.pot.shift.moz4C input_bond-AB.pot.deriv.TAbSL
>>>>>> ./TABLE/table_AB.xvg' (from tags convert_potential tab) dir
>>>>>> /usr/share/votca/scripts/inverse
>>>>>> >
>>>>>> > I mean, am i doing any mistake?
>>>>>> Is there an error? I don't see any error message above.
>>>>>> Just have a look at table_AB.xvg. The output above is mainly, so you
>>>>>> can see all the sub steps that have done.
>>>>>>
>>>>>> In short lines starting with "csg_get_interaction_property" read
>>>>>> values from your xml file (or use the default if empty)
>>>>>> Line with "Running subscript .." run a sub step e.g. interpolation,
>>>>>> extrapolation
>>>>>>
>>>>>> Christoph
>>>>>>
>>>>>> >
>>>>>> > I am attaching my bond.xml file here.
>>>>>> >
>>>>>> > Can you please help me with this.
>>>>>> >
>>>>>> > Thank you.
>>>>>> >
>>>>>> > Sanjeet
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> > --
>>>>>> > Join us on Slack: https://join.slack.com/t/votca/signup
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>>>>>> send an email to [email protected].
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>>>>>> .
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Christoph Junghans
>>>>>> Web: http://www.compphys.de
>>>>>>
>>>>>> --
>>>>>> Join us on Slack: https://join.slack.com/t/votca/signup
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>>>>>> .
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> *Sanjeet Kumar Singh*
>>>>>
>>>>> *Postdoctoral Fellow*
>>>>>
>>>>> *LPCM Lab.*
>>>>> *University De Sherbrooke*
>>>>> *Sherbrooke, Canada.*
>>>>>
>>>>> --
>>>>> Join us on Slack: https://join.slack.com/t/votca/signup
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>>>>>
>>>> To view this discussion on the web visit
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>>>>>
>>>>> <https://groups.google.com/d/msgid/votca/CABgeOec4V5xTeZ0vwNvzLNdKYp-SDzoCH-XEcgML729As5-NnA%40mail.gmail.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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