Dear Christoph,
I think that bond potentials seem to be good with U shape using
csg_call --options options.xml --ia-type bond --ia-name bond
convert_potential gromacs
The following potentials in figures are obtained from csg_call. I am
not sure of forces though. With all those potentials, now it does not run
even single iteration.
Started mdrun on rank 0 Tue Aug 30 15:10:53 2016
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
5.01406e+03 1.41421e+05 2.15701e+02 2.49642e+03 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
1.49147e+05 3.66788e+03 1.52815e+05 3.02256e+02 1.68470e+03
DD step 9 load imb.: force 6.7%
Not all bonded interactions have been properly assigned to the domain
decomposition cells
A list of missing interactions:
Tab. Angles of 856 missing 1
Molecule type 'TDM'
the first 10 missing interactions, except for exclusions:
Tab. Angles atoms 1 3 2 global 201 203 202
-------------------------------------------------------
Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
Source code file:
/home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec_top.c, line:
394
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
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Best regards,
Changwoon Jang
On Tue, Aug 30, 2016 at 2:54 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-08-30 12:33 GMT-06:00 Chang Woon Jang <[email protected]>:
> > Dear Christoph,
> >
> > It runs smoothly up to 12500 iterations. After that the error still
> exist
> > as follows. Luckily, 10K iterations do not produce the error.
> The below error means a bond got stretched more than 2.02391 nm, which
> seems a bit unphysical.
> You can look at your bond distributions if 2.02391 nm has a
> probability greater than 0.
> I guess, you will have to pick the min and max more carefully the xml
> file for the bonds when using csg_call.
> As rule of thumb min and max should lie on a downwards slopping, but
> not quite 0 yet, part of the distribution.
> After all the extrapolation csg_call does (see manual for details) the
> potentials should look like a deformed U or W, you can check that by
> look at the xvg output file.
>
> Christoph
> >
> >
> >
> > DD step 12499 load imb.: force 5.6%
> >
> > Step Time Lambda
> > 12500 6.25000 0.00000
> >
> > Energies (kJ/mol)
> > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb
> (SR)
> > 1.21732e+03 8.55168e+02 1.85141e+02 2.66780e+03
> 0.00000e+00
> > Potential Kinetic En. Total Energy Temperature Pressure
> (bar)
> > 4.92543e+03 3.80913e+03 8.73456e+03 3.13896e+02
> 1.21927e+03
> >
> >
> > Not all bonded interactions have been properly assigned to the domain
> > decomposition cells
> >
> > A list of missing interactions:
> > Tab. Dih. of 108 missing 1
> >
> > Molecule type 'JMT'
> > the first 10 missing interactions, except for exclusions:
> > Tab. Dih. atoms 1 2 3 4 global 927 928 929
> > 930
> >
> > -------------------------------------------------------
> > Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
> > Source code file:
> > /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec_top.c,
> line:
> > 394
> >
> > 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
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > Best regards,
> > Changwoon Jang
> >
> >
> > On Tue, Aug 30, 2016 at 2:22 PM, Chang Woon Jang <
> [email protected]>
> > wrote:
> >>
> >> Dear Christoph,
> >>
> >> Did you also change original bond and angle tables to gromacs format?
> >>
> >> If so, how do I determine the min and max values for bond and angle
> >> tables?
> >>
> >>
> >>
> >> Thank you.
> >>
> >> Best regards,
> >> Changwoon Jang
> >>
> >> On Tue, Aug 30, 2016 at 2:04 PM, Christoph Junghans <[email protected]
> >
> >> 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 <[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,
> >>> >>> >
> >>> >>> > --
> >>> >>> > You received this message because you are subscribed to the
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> >>> >>> > send
> >>> >>> > an
> >>> >>> > email to [email protected].
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> >>> >>>
> >>> >>>
> >>> >>>
> >>> >>> --
> >>> >>> Christoph Junghans
> >>> >>> Web: http://www.compphys.de
> >>> >>>
> >>> >>> --
> >>> >>> You received this message because you are subscribed to the Google
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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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> send
> >>> >> an
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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: [email protected]
> >
> >
> >
> >
> > --
> > 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
>
> --
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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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