2013/8/12 Chandan Choudhury <[email protected]>: > Dear votca users, > > I have used the following setting.xml file for interating the bonded as well > as non-bonded part. I couldnot suceed in doing the iteration. It gives me > the error : Fatal error: > A tabulated bond interaction table number 1 is out of the table range: r > 16.212738, between table indices 8106 and 8107, table length 3126 If the tables look ok, that might be a Gromacs problem. But isn't 16.21 a little too long for a bond?
> > For more information and tips for troubleshooting, please check the GROMACS > > > Kindly suggest me how do I rectify the error. > > ################################################## > <!--setting.xml--> > > <cg> > <bonded> > <!-- name of the interaction --> > <name>AB.bond</name> > <min>0.42</min> > <max>0.52</max> > <step>0.002</step> > <inverse> > <!-- target distribution --> > <target>AB.bond.tgt</target> > <gromacs> > <table>table_b0.xvg</table> > </gromacs> > </inverse> > </bonded> > <bonded> > <name>BC.bond</name> > <min>0.32</min> > <max>0.40</max> > <step>0.002</step> > <inverse> > <!-- target distribution --> > <target>BC.bond.tgt</target> > <gromacs> > <table>table_b1.xvg</table> > </gromacs> > </inverse> > </bonded> > <bonded> > <name>CD.bond</name> > <min>0.34</min> > <max>0.45</max> > <step>0.002</step> > <inverse> > <!-- target distribution --> > <target>CD.bond.tgt</target> > <gromacs> > <table>table_b2.xvg</table> > </gromacs> > </inverse> > </bonded> > <bonded> > <name>DB.bond</name> > <min>0.40</min> > <max>0.52</max> > <step>0.002</step> > <inverse> > <!-- target distribution --> > <target>DB.bond.tgt</target> > <gromacs> > <table>table_b3.xvg</table> > </gromacs> > </inverse> > </bonded> > <bonded> > <!-- name of the interaction --> > <name>BE.bond</name> > <min>0.32</min> > <max>0.40</max> > <step>0.002</step> > <inverse> > <!-- target distribution --> > <target>BE.bond.tgt</target> > <gromacs> > <table>table_b4.xvg</table> > </gromacs> > </inverse> > </bonded> > > <!-- example for a non-bonded interaction entry --> > <non-bonded> > <!-- name of the interaction --> > <name>A-A</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>A</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>A-A.dist.tgt</target> > <!-- update cycles --> > <do_potential>1 0 0</do_potential> > <!-- additional post processing of dU before added to potential --> > > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_A_A.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>A-B</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>B</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>A-B.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 1 0</do_potential> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_A_B.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>A-C</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>C</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>A-C.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 0 1</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_A_C.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>A-D</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>D</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>A-D.dist.tgt</target> > <!-- update cycles --> > <do_potential>1 0 0</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_A_D.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>A-E</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>E</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>A-E.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 1 0</do_potential> > <!-- additional post processing of dU before added to potential --> > > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_A_E.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>B-B</name> > <!-- types involved in this interaction --> > <type1>B</type1> > <type2>B</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>B-B.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 0 1</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_B_B.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>B-C</name> > <!-- types involved in this interaction --> > <type1>B</type1> > <type2>C</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>B-C.dist.tgt</target> > <!-- update cycles --> > <do_potential>1 0 0</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_B_C.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>B-D</name> > <!-- types involved in this interaction --> > <type1>B</type1> > <type2>D</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>B-D.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 1 0</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_B_D.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>B-E</name> > <!-- types involved in this interaction --> > <type1>B</type1> > <type2>E</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>B-E.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 0 1</do_potential> > <!-- additional post processing of U after dU added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_B_E.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>C-C</name> > <!-- types involved in this interaction --> > <type1>C</type1> > <type2>C</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>C-C.dist.tgt</target> > <!-- update cycles --> > <do_potential>1 0 0</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_C_C.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>C-D</name> > <!-- types involved in this interaction --> > <type1>C</type1> > <type2>D</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>C-D.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 1 0</do_potential> > <!-- additional post processing of dU before added to potential --> > > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_C_D.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>C-E</name> > <!-- types involved in this interaction --> > <type1>C</type1> > <type2>E</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>C-E.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 0 1</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_C_E.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>D-D</name> > <!-- types involved in this interaction --> > <type1>D</type1> > <type2>D</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>D-D.dist.tgt</target> > <!-- update cycles --> > <do_potential>1 0 0</do_potential> > <!-- additional post processing of dU before added to potential --> > > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_D_D.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>D-E</name> > <!-- types involved in this interaction --> > <type1>D</type1> > <type2>E</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>D-E.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 1 0</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_D_E.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <non-bonded> > <!-- name of the interaction --> > <name>E-E</name> > <!-- types involved in this interaction --> > <type1>E</type1> > <type2>E</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.30</min> > <max>2.25</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>E-E.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 0 1</do_potential> > <!-- additional post processing of dU before added to potential --> > > <post_add>convergence</post_add> > <post_add_options> > <convergence> > <weight> 1 </weight> > <what> dist</what> > </convergence> > </post_add_options> > > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_E_E.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > <!-- general options for inverse script --> > <inverse> > <!-- 480*0.00831451 gromacs units --> > <kBT>3.99096</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>6.25</table_end> > <grompp> > <bin> grompp_463</bin> > </grompp> > <mdrun> > <command> mdrun_463 </command> > <checkpoint>state.cpt</checkpoint> > </mdrun> > </gromacs> > <map> pc_new.xml </map> > <!-- these files are copied for each new run --> > <filelist>grompp.mdp topol.top table.xvg index.ndx table_a*</filelist> > <!-- do so many iterations --> > <iterations_max>1</iterations_max> > <convergence_check> > <type>default</type> > <limit>0.100</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> > </cg> > > > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Sat, Aug 10, 2013 at 12:16 PM, Chandan Choudhury <[email protected]> > wrote: >> >> Dear Christoph, >> Thanks for your response. >> >> I didnot find anything wrong in table_b1. The table length is 3126, there >> is no line 14359. I have also checked all the tables table_b*. They all look >> similar. Infact, when I rerun the grompp command and then mdrun, then in the >> error the table indices vary. >> I could not understand how to get rid of this. >> >> Chandan >> >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> >> On Fri, Aug 9, 2013 at 8:47 PM, Christoph Junghans <[email protected]> >> wrote: >>> >>> 2013/8/9 Chandan Choudhury <[email protected]>: >>> > Dear votca user, >>> > >>> > I am using the 1.3-dev version of version. >>> > I want to iterated the bond potential for my system. In doing so, I use >>> > the >>> > tabulated bond potential (table_b0.xvg) as the guess potential for the >>> > bonds. For angles, I generate tabulated angle potential. I use the >>> > table_A_A.xvg, table_A_B.xvg ..... as the non-bonded potential. >>> > >>> > When I just do the iteration of non-bonded part, my cg simulation >>> > proceeds >>> > smoothly. Problem occurs, when I try to incorprate the interation on >>> > bonded >>> > part. The simulation stops with the following error >>> > >>> > Fatal error: >>> > A tabulated bond interaction table number 1 is out of the table range: >>> > r >>> > 28.719402, between table indices 14359 and 14360, table length 3126 >>> > For more information and tips for troubleshooting, please check the >>> > GROMACS >>> > website at http://www.gromacs.org/Documentation/Errors >>> Have a look at table_b1.xvg, which VOTCA generates and see if it looks >>> ok or if there is anything wrong a line 14359. >>> >>> >>> > >>> > >>> > My initial coordinate is mapped from the atomistic trajectory. And this >>> > structure simulates without any problem when I only consider the >>> > non-bonded >>> > part. >>> > >>> > Any help/suggestion would be very helpful. >>> > >>> > Chandan >>> > >>> > -- >>> > Chandan kumar Choudhury >>> > NCL, Pune >>> > INDIA >>> > >>> > -- >>> > 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 http://groups.google.com/group/votca. >>> > For more options, visit https://groups.google.com/groups/opt_out. >>> > >>> > >>> >>> >>> >>> -- >>> 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 http://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >>> >> > > -- > 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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > > -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
