Dear VOTCA users, I am trying to modify my non-bonded potentials so as to get a better RDF plot. i wish to modify the non-bonded potentials between the head bead and the end bead of my coarse-grained molecule. I used the attached .xml and the .mdp file. I got following error while running the csg_inverse command: subscript /opt/votca1/share/votca/scripts/inverse/RDF_to_POT.pl Q0-C5.dist.tgt Q0-C5.pot.new.raw.JtH (from tags rdf pot) failed.
Please guide me what I should do Thanking You, Sincerely Arpita Srivastava Research Scholar, Dept. of Chemistry, IIT-Jodhpur. On Wed, Aug 31, 2016 at 5:28 PM, ArS <[email protected]> wrote: > Dear VOTCA users, > > I am trying to make modifications in my non-bonded potentials using > iterative Boltzmann method. I wish to modify the non-bonded potentials > between the head bead and the end bead of my coarse-grained molecule. I > created an xml file according to my need but while running the csg_inverse > command, I am getting an error as: > > > > # ERROR: > > # critical: 'cp conf.gro /home/iitj-ananya/Desktop/new- > cg-a1/a1-traj-AA/replicate-along-z/nb-corrections/step_000' failed # > > Please tell me how to fix this error. I am attaching my .xml also, have a > look at it and let me know if it contains any mistake. > > Thank You > ArS > > -- > 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. > -- 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.
grompp.mdp
Description: Binary data
<cg>
<non-bonded>
<name>Q0-C5</name>
<type1>Q0</type1>
<type2>C1</type2>
<min>0.31</min>
<max>0.36</max>
<step>0.01</step>
<inverse>
<target>rdf-com-head-btm_ste.xvg</target>
<do_potential>1 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential -->
<post_add></post_add>
<gromacs>
<table>table_Q0_C5.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>P2-C4</name>
<type1>P2</type1>
<type2>C1</type2>
<min>0.31</min>
<max>0.36</max>
<step>0.01</step>
<inverse>
<target>rdf-com-head-btm_ste.xvg</target>
<do_potential>0 1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential -->
<post_add></post_add>
<gromacs>
<table>table_P2_C4.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<inverse>
<kBT>2.35300633</kBT>
<program>gromacs</program>
<gromacs>
<equi_time>10</equi_time>
<table_bins>0.002</table_bins>
<pot_max>1000000</pot_max>
<table_end>12.0</table_end>
</gromacs>
<filelist>grompp.mdp topol.top table_b1.xvg table_b2.xvg table_b3.xvg table_b4.xvg table_b5.xvg table_a1.xvg table_a2.xvg table_a3.xvg table_a4.xvg table_b5.xvg table_b6.xvg table_b7.xvg table_b8.xvg table_a5.xvg table_a6.xvg table_a7.xvg index.ndx</filelist>
<iterations_max>100</iterations_max>
<method>ibi</method>
<scriptpath>$PWD</scriptpath>
<log_file>inverse.log</log_file>
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>
