On Sun, Jul 22, 2018 at 1:27 PM, 'Andrey Brukhno' via votca <[email protected]> wrote: > 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). The " rdf calculation is already done" tells me that this is not a run from scratch. Try a fresh run, because some chance in the xml don't get populated until the next iteration step. And grep for "csg_stat" (not rdf), you should see actually command, which got run, e.g.: "Running critical command 'csg_stat --nt 4 --options settings.xml --top topol.tpr --trj traj.xtc --begin 20 --first-frame 0' " >From that you can see if all the options are read as excepted.
Christoph > > 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. -- 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.
