2016-08-30 12:22 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
> Dear Christoph,
>
> Did you also change original bond and angle tables to gromacs format?
I only looked at the dihedral!
>
> If so, how do I determine the min and max values for bond and angle tables?
Basically you look at the distributions and find the well-sampled region.
For angle, usually 0 to pi works ok, but for the bond it is more hand tuning.
Christoph
>
>
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Tue, Aug 30, 2016 at 2:04 PM, Christoph Junghans <jungh...@votca.org>
> wrote:
>>
>> 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 <jungh...@votca.org>:
>> > 2016-08-29 15:19 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>> >> 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
>> >> <jungh...@votca.org>
>> >> wrote:
>> >>>
>> >>> 2016-08-29 13:32 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>> >>> > 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: cj...@drexel.edu
>> >>
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>> >
>> >
>> >
>> > --
>> > Christoph Junghans
>> > Web: http://www.compphys.de
>>
>>
>>
>> --
>> 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: cj...@drexel.edu
>
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--
Christoph Junghans
Web: http://www.compphys.de
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