Thanks for your reply Christoph. I did check it, but inverse.log does not contain sufficient info, see the extract below. I will be investigating it further to make sure I did not do anything stupid myself, although I haven't changed much for the test iteration except recompiling the tpr files for the newer version of Gromacs).
Andrey ----- $ grep rdf inverse.log ... cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr table_??.xvg index.ndx* conf.gro*' cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr table_??.xvg index.ndx* conf.gro*' cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr table_??.xvg index.ndx* conf.gro*' cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr table_??.xvg index.ndx* conf.gro*' cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr table_??.xvg index.ndx* conf.gro*' ‘sim_0/topol-rdf.tpr’ -> ‘./topol-rdf.tpr’ Calculating rdfs with csg_stat using 4 tasks Calculating average rdfs and its errors for interaction TCH-TCH rdf calculation is already done Calculating average rdfs and its errors for interaction TCH-TCO rdf calculation is already done Calculating average rdfs and its errors for interaction TCO-TCO rdf calculation is already done Calculating average rdfs and its errors for interaction TCH-PO rdf calculation is already done Calculating average rdfs and its errors for interaction TCH-NH rdf calculation is already done Calculating average rdfs and its errors for interaction TCO-PO rdf calculation is already done Calculating average rdfs and its errors for interaction TCO-NH rdf calculation is already done Calculating average rdfs and its errors for interaction PO-PO rdf calculation is already done Calculating average rdfs and its errors for interaction PO-NH rdf calculation is already done Calculating average rdfs and its errors for interaction NH-NH On Sun, Jul 22, 2018 at 1:26 PM, Christoph Junghans <[email protected]> wrote: > 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 a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/votca/l42VuhKqQb4/unsubscribe. > To unsubscribe from this group and all its topics, 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.
