On Tue, Jul 24, 2018 at 2:33 AM, 'Andrey Brukhno' via votca <[email protected]> wrote: > It seems that mapping files are only used for IBI. This absolutely correct, mapping files are currently only implemented for IBI and not for IMC, RE.
Christoph > > Andrey > > > On Tue, Jul 24, 2018 at 1:31 AM, Christoph Junghans <[email protected]> > wrote: >> >> On Mon, Jul 23, 2018 at 4:14 PM, 'Andrey Brukhno' via votca >> <[email protected]> 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. >> >> 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. >> >> >> >> 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 >> > >> > >> > Well, I can of course, but v1.4.1 does not use any special rdf.topol tag >> > (so >> > I have to introduce it myself): >> > >> > sim_prog="$(csg_get_property cg.inverse.program)" >> > >> > topol=$(csg_get_property cg.inverse.$sim_prog.topol) >> > [[ -f $topol ]] || die "${0##*/}: topol file '$topol' not found, >> > possibly >> > you have to add it to cg.inverse.filelist" >> > >> > traj=$(csg_get_property cg.inverse.$sim_prog.traj) >> > [[ -f $traj ]] || die "${0##*/}: traj file '$traj' not found" >> > >> > equi_time="$(csg_get_property cg.inverse.$sim_prog.equi_time)" >> > if [[ ${CSG_RUNTEST} ]] && csg_calc "$equi_time" ">" "0"; then >> > msg --color blue --to-stderr "Automatically setting equi_time to 0, >> > because CSG_RUNTEST was set" >> > equi_time=0 >> > fi >> > >> > first_frame="$(csg_get_property cg.inverse.$sim_prog.first_frame)" >> > >> > tasks=$(get_number_tasks) >> > msg "Calculating IMC statistics using $tasks tasks" >> > if is_done "imc_analysis"; then >> > echo "IMC analysis is already done" >> > else >> > #copy+resample all target dist in $this_dir >> > for_all "non-bonded bonded" do_external resample target >> > '$(csg_get_interaction_property inverse.target)' >> > '$(csg_get_interaction_property name).dist.tgt' >> > >> > critical csg_stat --do-imc --options "$CSGXMLFILE" --top "$topol" >> > --trj >> > "$traj" --begin $equi_time --first-frame $first_frame --nt $tasks >> > mark_done "imc_analysis" >> This is interesting, too! csg_stat for IMC is always called without >> mapping files. >> >> Christoph >> > fi >> > >> > >> >> >> >> >> >> > >> >> > Andrey >> >> > >> >> > On Monday, July 23, 2018 at 2:33:44 PM UTC+1, Christoph Junghans >> >> > wrote: >> >> >> >> >> >> On Mon, Jul 23, 2018 at 7:28 AM, 'Andrey Brukhno' via votca >> >> >> <[email protected]> wrote: >> >> >> > Christoph, >> >> >> > >> >> >> > I think I figured why there is no log msg for critical csg_stat in >> >> >> > calc_rdfgeneric.sh. >> >> >> > The fact is I override the inverse.sh script with the one having >> >> >> > this >> >> >> > (to >> >> >> > avoid all the frame numbers when reading trajectory files): >> >> >> > >> >> >> > log="${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 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>> >> >> >> > -- >> >> >> >> > 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 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.
