2016-08-30 12:33 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > 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 <changwoonj...@gmail.com> > 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 <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, >>> >>> > >>> >>> > -- >>> >>> > 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 votca+unsubscr...@googlegroups.com. >>> >>> > To post to this group, send email to votca@googlegroups.com. >>> >>> > Visit this group at https://groups.google.com/group/votca. >>> >>> > For more options, visit https://groups.google.com/d/optout. >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> Christoph Junghans >>> >>> Web: http://www.compphys.de >>> >>> >>> >>> -- >>> >>> 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 votca+unsubscr...@googlegroups.com. >>> >>> To post to this group, send email to votca@googlegroups.com. >>> >>> Visit this group at https://groups.google.com/group/votca. >>> >>> For more options, visit https://groups.google.com/d/optout. >>> >> >>> >> >>> >> >>> >> >>> >> -- >>> >> 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 >>> >> >>> >> -- >>> >> 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 votca+unsubscr...@googlegroups.com. >>> >> To post to this group, send email to votca@googlegroups.com. >>> >> Visit this group at https://groups.google.com/group/votca. >>> >> For more options, visit https://groups.google.com/d/optout. >>> > >>> > >>> > >>> > -- >>> > Christoph Junghans >>> > Web: http://www.compphys.de >>> >>> >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >>> >>> -- >>> 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 votca+unsubscr...@googlegroups.com. >>> To post to this group, send email to votca@googlegroups.com. >>> Visit this group at https://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> -- >> 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 > > > > > -- > 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 > > -- > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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