On Mon, Jul 23, 2018 at 2:22 AM, Christoph Junghans <[email protected]> wrote:
> 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. > > I knew you were going to say this... As a matter of fact, there is no such message from calc_rdf_generic.sh, but instead: msg "Calculating rdfs with csg_stat using $tasks tasks" critical csg_stat --nt $tasks --options "$CSGXMLFILE" --top "$topol" --trj "$traj" --begin $equi_time --first-frame $first_frame ${error_opts} ${maps:+--cg ${maps}} mark_done "rdf_calculation${suffix}" so I had to add this after the msg and before the csg_stat call: echo "Doing: critical csg_stat --nt $tasks --options "$CSGXMLFILE" --top "$topol" --trj "$traj" --begin $equi_time --first-frame $first_frame ${error_opts} ${maps:+--cg ${maps}}" This shows me that topol-rdf.tpr is actually used (extract from inverse.log): Make update for ibi Calculating rdfs with csg_stat using 4 tasks Doing: critical csg_stat --nt 4 --options /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-freeN-dihs_CG-fits1-151cT/dopc_cg-int-map11.xml --top topol-rdf.tpr --trj traj.xtc --begin 0 --first-frame 0 --block-length 1000000 --ext dist.block --cg /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-freeN-dihs_CG-fits1-151cT/dopc_cg-map11.xml; begin to calculate distribution functions However, the distributions are still wrong, and I am lost now as to which program to blame (again all the initial files are the same as in my previous iteration). I compared the outputs of `gmx dump topol-rdf.tpr' and `gmx dump topol.tpr' generated with the new Gromacs and everything seems alright, the relevant differences in exclusion lists are there. The problem is also that the original calculation was done on a cluster more than a year ago, so I cannot reproduce exactly all the installation setup, not on my desktop anyway. But I know that those calculations were correct and well converged. So something should have changed somewhere within the newly installed Gromacs/VOTCA combination. Andrey 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 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. 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