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
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
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>> > email to [email protected].
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>> >
>> >
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>> --
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>>
>>
>
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