Not only that (mapping) but also calculation of distributions with errors
seems to be only supported for IBI.
("seems" because I only checked calc_rdf_generic.sh, imc_stat_generic.sh
and update_re.sh)
Andrey
On Tuesday, July 24, 2018 at 12:26:58 PM UTC+1, Christoph Junghans wrote:
>
> On Tue, Jul 24, 2018 at 2:33 AM, 'Andrey Brukhno' via votca
> <[email protected] <javascript:>> 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]
> <javascript:>>
> > wrote:
> >>
> >> On Mon, Jul 23, 2018 at 4:14 PM, 'Andrey Brukhno' via votca
> >> <[email protected] <javascript:>> 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>
> >> >> >> >> >> >> >> > -----------
> >> >> >> >> >> >> >> >
> >> >> >> >> >> >> >> > --
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> >>
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