On Mon, Jul 23, 2018 at 7:25 AM, Christoph Junghans <[email protected]> wrote: > On Mon, Jul 23, 2018 at 7:02 AM, 'Andrey Brukhno' via votca > <[email protected]> wrote: >> >> On Mon, Jul 23, 2018 at 1:46 PM, Christoph Junghans <[email protected]> >> wrote: >>> >>> On Mon, Jul 23, 2018 at 6:39 AM, 'Andrey Brukhno' via votca >>> <[email protected]> wrote: >>> > 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! >>> This behavior hasn't changed for long time and was certainly the same >>> in v1.3 as well. >> >> >> I am only reporting my experience: version 1.3 (installed on our cluster 8 >> Feb 2015) did not need any extra exclusion definitions (nrex) nor list and I >> had no problem obtaining correct distributions with topol-rdf.tpr only (the >> number provided by [moleculetype] is 10). >> But now, as of v1.41, the distributions correspond to exclusions starting >> with 1-4 intra-molecular pairs (the number provided by [moleculetype] is 3). >> >> Since I did not have any issue before, I did not care about generating >> exclusion lists in addition to tpr files. > Well then don't specify a mapping or a secondary tpr file. Both > together don't make much sense. > >> >>> >>> When using a mapping file, exclusions get generated for each bond, >>> angle and dihedral interaction in the mapping file. >>> >>> Why are using a mapping file to begin with? >> >> >> Good question! >> Well, the manual advises to use cg.inverse.map tag with a one-to-one mapping >> xml file for iterative methods even when optimising only non-bonded >> interactions (and I recall having problems without this tag!), so I have: > I guess you are referring to section 7.3.2, but that is referring to > IMC (not IBI). > And even then, that has already been improved a while (pre-v1.3) ago, > so that section should probably get removed unless you remember a > reason why it is needed for IMC. https://github.com/votca/csg-manual/pull/8
> >> >> <map> >> <DESC>Special mapping file for rdf calculations needed for bonded >> interactions</DESC> >> dopc_cg-map11.xml >> </map> >> >> and of course I do not do anything special about the csg_stat call in >> calc_rdf_generic.sh, so it does what it does. >> >> Andrey >> >>> >>> Christoph >>> > >>> > 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 >>> > "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 -- 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.
