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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>> >> > For more options, visit https://groups.google.com/d/optout.
>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >>
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
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