On Mon, Jul 23, 2018 at 1:17 PM, Christoph Junghans <[email protected]> wrote:
> On Mon, Jul 23, 2018 at 2:39 AM, 'Andrey Brukhno' via votca > <[email protected]> wrote: > > > > 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}" > Well the "critical" function includes the print statement: > critical() { > [[ $quiet = "no" ]] && echo "Running critical command '$*'" >&2 > "$@" || die "${FUNCNAME[0]}: '$*' failed" > } > So I am not sure when that got lost in your case. > > > > 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. > You can see what VOTCA has with: > csg_dump --top topol-rdf.tpr --cg dopc_cg-map11.xml > OK, but its output does not contain any info about the exclusions. > > Remember, if you are using a mapping file ("--cg" option) exclusions > from the topology file are ignored and the ones from the mapping file > are used instead. > Alright, this must be the root of my problem! Apparently, in v1.3 csg_stat would take the exclusions from tpr, not xml, because I never provided any exclusion list in any xml file, but it did work correctly! I will look into this again. Andrey > > Christoph > > > > 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. > > 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 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