2016-01-25 15:07 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Votca Users, > > I haver tried to run ibi simulation with my own polymer system. The > error message is > > ------------------------------------------------------- > Program gmx, VERSION 5.0.8-dev-20151014-1f04b58 > Source code file: > /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/fileio/futil.cpp, line: > 790 > > Fatal error: > Library file table_b1.xvg not found in current dir nor in default > directories. > (You can set the directories to search with the GMXLIB path variable) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > > In my setting.xml, I did not include table_b1.xvg or table_a1.xvg. Instead, > I did include filelist section of bond and angle potentials calculated from > csg_boltzmann. I do not know why the error message complains "Library file > table_b1.xvg not found in current dir nor in default directories." > > I have four types of beads (A, B, C, D). The first molecule is A-B-A > configuration and the second molecule is C-D-C configuration. Therefore, I > need include A-B and C-D bond potentials and A-B-A and C-D-C angle > potentials. As you can see my setting file, I listed those potentials in > <filelist> section. > > Would you give me some advise? > > <!-- general options for inverse script --> > <inverse> > <!-- 300*0.00831451 gromacs units --> > <kBT>2.49435</kBT> > <!-- use gromacs as simulation program --> > <program>gromacs</program> > <!-- gromacs specific options --> > <gromacs> > <!-- trash so many frames at the beginning --> > <equi_time>10</equi_time> > <!-- grid for table*.xvg !--> > <table_bins>0.002</table_bins> > <!-- cut the potential at this value (gromacs bug) --> > <pot_max>1000000</pot_max> > <!-- extend the tables to this value --> > <table_end>2.5</table_end> > </gromacs> > <!-- these files are copied for each new run --> > <filelist>grompp.mdp topol.top table.xvg ABAangle.xvg CDCangle.xvg > ABbond.xvg CDbond.xvg index.ndx</filelist> If you don't iterate over the bonded interaction, you will need to add "table_b1.xvg" to this list.
Just looking at the other files listed, ABAangle.xvg CDCangle.xvg ABbond.xvg CDbond.xvgCDbond.xvg doesn't seem to follow gromacs' naming scheme. You will have to name them something like table_a1.xvg, table_a2.xvg, table_b1.xvg and table_b2.xvg. Christoph > <!-- do so many iterations --> > <iterations_max>500</iterations_max> > <convergence_check> > <type>default</type> > <limit>0.001</limit> > </convergence_check> > <!-- ibm: inverse biltzmann imc: inverse monte carlo --> > <method>ibi</method> > <!-- write log to this file --> > <log_file>inverse.log</log_file> > <!-- write restart step to this file --> > <restart_file>restart_points.log</restart_file> > </inverse> > > > > Thank you very much. > > > 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.
