>> >> > 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.
>
Do you mean the cg.inverse.map tag is not needed anymore in .xml for both
IBI and IMC nowadays?
Or should I still include the tag for IMC? Because as of now IMC (and also
RE) produces wrong distributions too.
Andrey
>
> >
> > 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.
>
> >
> > <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>
> >> >> >> >> > -----------
> >> >> >> >> >
> >> >> >> >> > --
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> >> >> >> >> > send
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> >> >> >> >> > email to [email protected].
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> >> >> >> >> > Visit this group at https://groups.google.com/group/votca.
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> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Christoph Junghans
> >> >> >> >> Web: http://www.compphys.de
> >> >> >> >>
> >> >> >> >> --
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> >> >> >> >
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> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Christoph Junghans
> >> >> >> Web: http://www.compphys.de
> >> >> >>
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> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >>
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> >> Web: http://www.compphys.de
> >>
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