On Mon, Jul 23, 2018 at 5:26 PM, 'Andrey Brukhno' via votca <[email protected]> wrote: > > > On Monday, July 23, 2018 at 8:18:39 PM UTC+1, Andrey Brukhno wrote: >> >> On Monday, July 23, 2018 at 3:17:49 PM UTC+1, Christoph Junghans wrote: >>> >>> On Mon, Jul 23, 2018 at 7:41 AM, 'Andrey Brukhno' via votca >>> <[email protected]> wrote: >>> > In this case, it's not an error message which is lost ;) Why does it go >>> > to >>> > stderr at all? >>> The code has the reason right there: >>> #print this message to stderr because $(critical something) is used very >>> often >>> >>> > Moreover, if I try to run the iteration a second time, everything >>> > including >>> > errors is reported back >>> Well that is good, nevertheless we just spend 5 E-Mails back and >>> forth, hunting down a bug you introduced yourself. >>> And I now recall you made that change to filter gromacs "Read frame >>> XXX" message, which is fixed when using a newer gromacs version >>> (>=2016.3), see: >>> >>> https://github.com/votca/csg/commit/155eb770873a6f65bac372c9f8c5efc9f3a4be75 >>> >>> > >>> > Anyway, my primary issue is not about messages, but to make it work >>> > correctly for distributions. >>> Like I said in the other email if section 7.3.2 is right, a mapping >>> file might be needed only for IMC, but even that I think is not true >>> anymore in v1.3.1. >> >> >> My test IMC iteration went through without tagging the 1:1 CG map file. >> >>> >>> So you need to figure out, which exclusions you want to read the ones >>> from the mapping file or the ones the tpr. >>> For the former specify a mapping file or the latter don't. >> >> >> OK, I preferred the exclusions from topol-rdf.tpr (which appears to work >> now for IBI), so I skipped the map tags in my settings file for IMC too. >> However, the distributions are still wrong in the case of IMC. > > > As a matter of fact including a 1:1 topology xml where all the > intra-molecular pairs are counted as bonded does not affect the exclusion > list (so only tpr file matters) for csg_dump: > > 1) the case where topol.tpr has nrexcl = 3 and topol-map11-rdf.xml defines > all pairs as bonded > >> csg_dump --top topol.tpr --map topol-map11-rdf.xml --excl > Reading file topol.tpr, VERSION 2018.2 (single precision) > I have 12 beads in 1 molecule > > List of exclusions: > 1 2 3 4 > 2 3 4 9 > 3 4 9 10 11 > 4 8 9 10 11 12 > 5 6 7 8 > 6 7 8 10 > 7 8 9 10 > 8 9 10 11 > 9 10 11 12 > 10 11 12 > 11 12 > > 2) the case where topol.tpr has nrexcl = 3 and no topol-map11-rdf.xml is > used > >> csg_dump --top topol.tpr --excl > Reading file topol.tpr, VERSION 2018.2 (single precision) > I have 12 beads in 1 molecule > > List of exclusions: > 1 2 3 4 > 2 3 4 9 > 3 4 9 10 11 > 4 8 9 10 11 12 > 5 6 7 8 > 6 7 8 10 > 7 8 9 10 > 8 9 10 11 > 9 10 11 12 > 10 11 12 > 11 12 > 13 14 15 16 > 14 15 16 21 > 15 16 21 22 23 > 16 20 21 22 23 24 > 17 18 19 20 > 18 19 20 22 > 19 20 21 22 > 20 21 22 23 > 21 22 23 24 > 22 23 24 > 23 24 > > 3) the case where topol-rdf.tpr has nrexcl = 10 so all pairs within a chain > are excluded from RDF calculation > >> csg_dump --top topol-rdf.tpr --excl > Reading file topol-rdf.tpr, VERSION 2018.2 (single precision) > I have 12 beads in 1 molecule > > List of exclusions: > 1 2 3 4 5 6 7 8 9 10 11 12 > 2 3 4 5 6 7 8 9 10 11 12 > 3 4 5 6 7 8 9 10 11 12 > 4 5 6 7 8 9 10 11 12 > 5 6 7 8 9 10 11 12 > 6 7 8 9 10 11 12 > 7 8 9 10 11 12 > 8 9 10 11 12 > 9 10 11 12 > 10 11 12 > 11 12 >
I am quite sure what you want to tell us with that comparison! If you want to achieve the same as nrexcl=10 with a mapping file, you will need to add 12*11/2=66 bonds between all possible pairs to that mapping file. Christoph >> >> >>> >>> >>> And then you can use csg_dump with or without --cg option to check the >>> exclusions! >>> $ csg_dump --top topol.tpr --excl >>> or >>> $ csg_dump --top topol.tpr --excl --cg mapping.xml. >>> >>> Christoph >>> >>> > >>> > Andrey >>> > >>> > On Monday, July 23, 2018 at 2:33:44 PM UTC+1, Christoph Junghans wrote: >>> >> >>> >> On Mon, Jul 23, 2018 at 7:28 AM, 'Andrey Brukhno' via votca >>> >> <[email protected]> wrote: >>> >> > Christoph, >>> >> > >>> >> > I think I figured why there is no log msg for critical csg_stat in >>> >> > calc_rdfgeneric.sh. >>> >> > The fact is I override the inverse.sh script with the one having >>> >> > this >>> >> > (to >>> >> > avoid all the frame numbers when reading trajectory files): >>> >> > >>> >> > log="${PWD}/${log##*/}" >>> >> > export CSGLOG="$log" >>> >> > if [[ -f $CSGLOG ]]; then >>> >> > exec 3>&1 4>&2 >> "$CSGLOG" 2>&1 >>> >> > echo -e "\n\n##################################" >>> >> > # echo "# Appending to existing logfile #" >>> >> > echo "# Appending to logfile (+errors) #" >>> >> > echo -e "##################################\n\n" >>> >> > msg --color blue "Appending to existing logfile (+errors) >>> >> > ${CSGLOG##*/}" >>> >> > else >>> >> > exec 3>&1 4>&2 >> "$CSGLOG" 2>/dev/null >>> >> > echo -e "\n\n##################################" >>> >> > echo "# Creating new logfile (-errors) #" >>> >> > echo -e "##################################\n\n" >>> >> > msg "For a more verbose log see: ${CSGLOG##*/} (or >>> >> > csg_inverse.log)" >>> >> > fi >>> >> > >>> >> > This worked before and did not affect the workflow. >>> >> Glad, you found it and it is not VOTCA's original code. >>> >> I remember now that you did this modification for a reason, which I >>> >> didn't like exactly because error message will get lost. >>> >> >>> >> Anyhow, well in conclusion if you send the errors to dev/null, you >>> >> won't see some messages (like critical) in the log file. >>> >> >>> >> Christoph >>> >> > >>> >> > Andrey >>> >> > >>> >> > On Mon, Jul 23, 2018 at 1:50 PM, Christoph Junghans >>> >> > <[email protected]> >>> >> > wrote: >>> >> >> >>> >> >> On Mon, Jul 23, 2018 at 6:46 AM, 'Andrey Brukhno' via votca >>> >> >> <[email protected]> wrote: >>> >> >> > Sorry, I forgot - below is the output of `grep critical >>> >> >> > inverse.log' >>> >> >> > for >>> >> >> > one >>> >> >> > iteration: >>> >> >> > >>> >> >> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp >>> >> >> > -p >>> >> >> > topol.top >>> >> >> > -o topol.tpr -c conf.gro' >>> >> >> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp >>> >> >> > -p >>> >> >> > topol.top >>> >> >> > -o topol.tpr -c conf.gro' >>> >> >> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp >>> >> >> > -p >>> >> >> > topol.top >>> >> >> > -o topol.tpr -c conf.gro' >>> >> >> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp >>> >> >> > -p >>> >> >> > topol.top >>> >> >> > -o topol.tpr -c conf.gro' >>> >> >> > Running critical command 'mpirun -n 4 mdrun_mpi -s topol.tpr -c >>> >> >> > confout.gro >>> >> >> > -o traj.trr -x traj.xtc -cpi state.cpt -maxh 47.8289 -multidir >>> >> >> > sim_0 >>> >> >> > sim_1 >>> >> >> > sim_2 sim_3 -tablep table.xvg -tableb table_b1.xvg table_b2.xvg >>> >> >> > table_b3.xvg >>> >> >> > table_b4.xvg table_b5.xvg table_a1.xvg table_a2.xvg table_a3.xvg >>> >> >> > table_a4.xvg table_a5.xvg table_d1.xvg table_d2.xvg table_d3.xvg >>> >> >> > table_d4.xvg table_d5.xvg table_d6.xvg' >>> >> >> > Doing: critical csg_stat --nt 4 --options >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-freeN-dihs_CG-fits1-151cNT/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-fits1-151cNT/dopc_cg-map11.xml; >>> >> >> > >>> >> >> > As you can see, the only mention of `critical csg_stat' is due to >>> >> >> > my >>> >> >> > addition of echo. >>> >> >> Well, the other lines with "Running critical command" show that the >>> >> >> logging actually works. >>> >> >> Did you overload calc_rdf_generic.sh with your own version? >>> >> >> Otherwise, I would say your installation is bourked up. >>> >> >> >>> >> >> Christoph >>> >> >> > >>> >> >> > Andrey >>> >> >> > >>> >> >> > On Monday, July 23, 2018 at 1:17:32 PM UTC+1, Christoph Junghans >>> >> >> > 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 >>> >> >> >> >>> >> >> >> 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. >>> >> >> >> >>> >> >> >> 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 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. >>> >>> >>> >>> -- >>> 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. -- 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.
