Hi,
thanks for sending the potentials.
Here is what I did:
$ ls table_d*.txt
table_d1.txt table_d2.txt table_d3.txt table_d4.txt
# These are the potentials out of csg_boltzmann
$ cat table_d.xml
<cg>
<bonded>
<!-- name of the interaction -->
<name>dihedral</name>
<min>-3.141</min>
<max>3.141</max>
<step>0.001</step>
</bonded>
<inverse>
<gromacs>
<pot_max>1e8</pot_max>
<table_bins>0.001</table_bins>
</gromacs>
</inverse>
</cg>
$ for i in table_d*.txt; do csg_call --options table_d.xml --ia-type
dihedral --ia-name dihedral --sloppy-tables convert_potential gromacs
$i ${i%.txt}.xvg; done
This basically does:
csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
--sloppy-tables convert_potential gromacs table_d1.txt table_d1.xvg
csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
--sloppy-tables convert_potential gromacs table_d2.txt table_d2.xvg
csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
--sloppy-tables convert_potential gromacs table_d3.txt table_d3.xvg
csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
--sloppy-tables convert_potential gromacs table_d4.txt table_d4.xvg
Please note you need the "--sloppy-tables" option as you want to
ignore the third column of table_d1.txt
Alternatively you could replace the 3rd column by "i":
$ awk '/^[^#]/{print $1,$2,"i"}' table_d1.txt > fixed_table_d1.txt
Then a I ran gromacs
$ gmx mdrun -tableb table_[abd]*.xvg -v
Please mind that this is gromacs 2016. which is why you need the
"-tableb" option. (Gromacs 5.0 was made obsolete a while back by its
developers.)
Seems to work for at least 10k steps.
Cheers,
Christoph
2016-08-29 20:52 GMT-06:00 Christoph Junghans <[email protected]>:
> 2016-08-29 15:19 GMT-06:00 Chang Woon Jang <[email protected]>:
>> Dear Christoph,
>>
>> Can I run ibi without dihedrals? Actually, I do not need dihedral
>> potentials even though CG molecules have dihedrals. Or, any suggestions for
>> debugging the dihedrals. Actually, the warning signs disappeared but I have
>> still the same Fatal error.
> Please send me the table and the xml off-list and I will have a look.
>
> And of course you can run IBI on a subset of the interactions, see
> <https://github.com/votca/csg-tutorials/tree/master/hexane/ibi>
> In this example only the non-bonded interactions are iterated.
>
> Christoph
>>
>> Thank you.
>>
>> Best regards,
>> Changwoon Jang
>>
>> On Mon, Aug 29, 2016 at 4:30 PM, Christoph Junghans <[email protected]>
>> wrote:
>>>
>>> 2016-08-29 13:32 GMT-06:00 Chang Woon Jang <[email protected]>:
>>> > Dear Votca Users,
>>> >
>>> > I have four dihedral distributions directly from csg_boltzmann.
>>> > However,
>>> > only one dihedral distribution gives waning sign during IBI run as
>>> > follows.
>>> >
>>> > WARNING: For the 359 non-zero entries for table 0 in table_d1.xvg the
>>> > forces
>>> > deviate on average 196% from minus the numerical derivative of the
>>> > potential
>>> That means something went wrong in the table conversion!
>>> >
>>> >
>>> >
>>> > Then, the IBI fails with Fatal error: 1 of the 1720 bonded interactions
>>> > could not be calculated because some atoms involved moved further apart
>>> > than
>>> > the multi-body cut-off distance (2.02391 nm) or the two-body cut-off
>>> > distance (2.02391 nm), see option -rdd, for pairs and tabulated bonds
>>> > also
>>> > see option -ddcheck
>>> That is most likely due to the above warning.
>>> >
>>> >
>>> > I am not sure why only one dihedral gives this warning and prevent IBI
>>> > run.
>>> > Do you have any comments on that?
>>> IBI for dihedral interactions is a bit tricky and not very well
>>> testing in VOTCA, so you will need to do a bit a debugging on your
>>> side.
>>>
>>> Christoph
>>>
>>> >
>>> > I have converted dihedral distribution radian to angle (only first
>>> > column)
>>> > due to the ibi requirement just using unit convert x*180/3.14 (x is
>>> > radian).
>>> >
>>> > Thank you.
>>> >
>>> > Best regards,
>>> > Changwoon Jang,
>>> >
>>> > --
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>>>
>>>
>>>
>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>>>
>>> --
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>>
>>
>>
>>
>> --
>> Best regards,
>> Changwoon Jang,
>>
>> Postdoctoral Research Fellow
>> Department of Chemical & Biological Engineering, Drexel University
>> 3141 Chestnut Street, Philadelphia, PA 19104
>>
>> Voice: (662) 617-2267
>> E-mail: [email protected]
>>
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>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
--
Christoph Junghans
Web: http://www.compphys.de
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