Hi Christoph,
Thank you for your suggestions. Now, I am able to get the LAMMPS table.
But, now I have some other doubt regarding the min, max, table_begin, and
table_end.
I am trying to get the potential for a bond using csg_boltzmann. The
distribution function for this bond obtained using csg_boltzmann shows
values ranging from 0.292337 to 0.351548.
Now, I am using the bond distribution obtained in the last step to get the
bonded potential. Again here, the min and max values used in the
boltzmann_cmds file is similar to the boundary values obtained from bonded
distribution file i.e. 0.292337 to 0.351548.
Then, I am converting the bonded potential to lammps table using the
bond.xml script shown below:
<cg>
<bonded>
<!-- FIRST BOND TYPE -->
<name>bond-AB</name>
<min>0.300337</min>
<max>0.343548</max>
<step>0.001</step>
<inverse>
<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>0.2</table_begin>
<table_end>0.35</table_end>
<table_bins>0.001</table_bins>
</lammps>
</inverse>
</bonded>
<inverse>
<program>lammps</program>
</inverse>
</cg>
Here, i have used the min as 0.300337 (0.292337 + 0.008) and max as
(0.351548 - 0.008) to leave room for interpolation . Is this correct?
Or, am I setting some incorrect values here?
Thank you.
Sanjeet
On Sunday, September 11, 2022 at 8:15:18 PM UTC-4 Christoph Junghans wrote:
> 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
>>>>>>>> > ---
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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/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
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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
>>>>>>
>>>>> --
>>>> Join us on Slack: https://join.slack.com/t/votca/signup
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>>>>
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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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