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 Google > >>> > Groups > >>> > "votca" group. > >>> > To unsubscribe from this group and stop receiving emails from it, > send > >>> > an > >>> > email to [email protected]. > >>> > To post to this group, send email to [email protected]. > >>> > 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 [email protected]. > >>> To post to this group, send email to [email protected]. > >>> 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: [email protected] > >> > >> -- > >> 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 [email protected]. > >> To post to this group, send email to [email protected]. > >> 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 [email protected]. > To post to this group, send email to [email protected]. > 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: [email protected] -- You received this message because you are subscribed to the Google Groups "votca" group. 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