On Sat, Jul 21, 2018 at 9:01 PM, 'Andrey Brukhno' via votca <[email protected]> wrote: > Hello, > > I encountered a very strange (looks like legacy) issue with v1.4.1. > In my earlier IBI iterations (with v1.3) I normally used special > topol-rdf.tpr which was different from normal CG simulation topol.tpr by not > including the intra-molecular pairs in the RDF stats (done by csg_stat). I > wanted to make sure my previous results are reproduced by v1.4.1, so copied > all the initialisation files into a new directory and tried to run once > again. After the very first iteration I checked the obtained RDFs and they > were all wrong - corresponding to normal topol.tpr (including intra-pairs) > and not topol-rdf.tpr (excluding intra-pairs)! > > I guess there might have been changes made to locations or names of tags in > settings.xml between the VOTCA versions, but I could not identify those > changes by referring to the most recent manual (both v1.4.1 and development > versions). > > Below is the relevant extract from my settings.xml file. > > Any clue, hint, advice are most welcome! We haven't changes any tags in IBI since v1.4.1 and the special topology for IBI can be set by cg.inverse.<sim_prog>.rdf.topol, which you did below. You could try "grep csg_stat inverse.log" to figure out if the right topology got appended to the command line of csg_stat.
Christoph > > Thanks in advance. > Andrey > > ----------- > <gromacs> > <grompp> > <bin>gmx grompp</bin> > <!--opts></opts--> > </grompp> > <mdrun> > <!--command>grmx-vtc-rerun.sh</command--> > <!--command>mpirun -lsf mdrun_mpi</command--> > <!--opts>-multidir sim_0 sim_1 sim_2 sim_3</opts--> > <command>mpirun -n 4 mdrun_mpi</command> > <opts>-multidir sim_0 sim_1 sim_2 sim_3 -tablep table.xvg -tableb > table_b?.xvg table_a?.xvg table_d?.xvg</opts> > </mdrun> > <!--mdrun><opts>-nt 2</opts></mdrun--> > <!-- trash so many frames at the beginning --> > <equi_time>0</equi_time> > <!-- grid for table*.xvg !--> > <table_bins>0.001</table_bins> > <!-- cut the potential at this value (gromacs bug) --> > <pot_max>10000</pot_max> > <!-- extend the tables to this value --> > <table_end>2.5</table_end> > <initial_configuration>maindir</initial_configuration> > <rdf> > <block_length><DESC>Length of the block for the error > analysis</DESC> > 1000000 > </block_length> > <map><DESC>Special mapping file for rdf calculations needed for > bonded interactions</DESC> > dopc_cg-map11.xml > </map> > <topol><DESC> Gromacs binary topol (tpr) file to be used for > csg_stat</DESC> > topol-rdf.tpr > </topol> > <with_errors>yes<DESC>calculate error on the rdf: yes/no</DESC> > </with_errors> > </rdf> > </gromacs> > ----------- > > -- > 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.
