On Sun, Sep 11, 2022 at 2:28 PM Sanjeet Singh <[email protected]> wrote:
> 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>
>
Well the cg.inverse.program is NOT an interaction property, but a global
one, you will have to leave that line in the block below.
Think about it is this way, bond.xml could contain multiple interaction and
all interaction properties (csg_get_interaction_property) are inside a
<bond> or <non-bonded> block and these can be different for each
interaction, while the global properties (csg_get_property) live in the
<cg> block out side of the <bond> block.
The output will tell if it is a global property (line starts
with csg_get_property) or an interaction specific one
(csg_get_interaction_property).
<!--<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
>
That looks fine, I think you can also do
$ csg_call --ia-type bond --ia-name bond-AB --options bond.xml
prepare_single ibi
to do the same. And provide the to be inverted distribution in the
inverse.target interaction property of the xml file.
For iterative boltzmann inversion csg_inverse will also do boltzmann
inversion in the initial step as well.
Bonded interactions are always a bit flaky, so doing it manually might be
better.
>
> 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.
>
In most cases you want to do a boltzmann inversion on a certain range
(where the distribution is >0), but then write out a table that is much
longer (up to the interaction cutoff) or finer grained (finer table_bins
than the bin size you want to the inversion on - for statistics reasons),
hence VOTC has both.
Christoph
> 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
>>>>>>> > ---
>>>>>>> > 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/f13d79c3-fcf7-4f7d-b608-01546106f1b2n%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.
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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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>>>>>> send an email to [email protected].
>>>>>>
>>>>> To view this discussion on the web visit
>>>>>> https://groups.google.com/d/msgid/votca/CABgeOec4V5xTeZ0vwNvzLNdKYp-SDzoCH-XEcgML729As5-NnA%40mail.gmail.com
>>>>>> <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
>>>>>
>>>> --
>>> 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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>
--
Christoph Junghans
Web: http://www.compphys.de
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