Am Mittwoch, 15. April 2020 14:00:32 UTC+2 schrieb Christoph Junghans: > > > > On Wed, Apr 15, 2020 at 05:56 Wolfgang Verestek <[email protected] > <javascript:>> wrote: > >> >> >> Am Mittwoch, 15. April 2020 13:52:01 UTC+2 schrieb Wolfgang Verestek: >>> >>> >>> >>> Am Dienstag, 14. April 2020 19:21:07 UTC+2 schrieb Christoph Junghans: >>>> >>>> >>>> >>>> On Tue, Apr 14, 2020 at 8:40 AM Wolfgang Verestek wrote: >>>> >>>>> Dear Christoph, >>>>> >>>>> it seems to me, that the bonds in topology.xml do not influence the >>>>> result of csg_stat. On contrary, i got the same results regardless of >>>>> bonds >>>>> being in topology.xml or not. The same is true for for wrapped or >>>>> unwrapped >>>>> coordinates. The only thing that did change the result was changing the >>>>> cell size in the conf.gro by factor of 10 in each dimenstion which looks >>>>> like the nonperiodic results from Ovito (but made it necessary to scale >>>>> by >>>>> a factor of 1000 to be in the same range of the plot). Furthermore, i >>>>> confirmed the results of Ovito by VMD. The nonperiodic calculation in VMD >>>>> oversitmates the first peak somewhat, but otherwise the results are in >>>>> good >>>>> agreement. The results don't match perfectly, but as i don't know how >>>>> exactly VMD or Ovito compute the RDF i guess the match is good enough and >>>>> the drop in the periodic VMD plot should be due to some other reason >>>>> (maybe >>>>> the g(r) plugin is limited to 3/4 cell lengt or sth.). >>>>> regarding scg_stat it still seems to me that the tail is smoothed or >>>>> periodic images in different directions are omitted. Could that be? I can >>>>> provide the files f necessary. >>>>> >>>> Ok now I am getting really confused, I just did a quick comparison of >>>> gmx rdf and csg_stat and the results are right on top of each other. >>>> >>>> Could you do me a favor and try to follow: >>>> ``` >>>> apt-get install gromacs >>>> cp /usr/share/gromacs/top/spc216.gro . >>>> wget >>>> https://raw.githubusercontent.com/votca/csg/master/src/tools/references/spce/sources/grompp.mdp >>>> wget >>>> https://raw.githubusercontent.com/votca/csg/master/src/tools/references/spce/sources/topol.top >>>> gmx grompp -c spc216.gro -maxwarn 1 >>>> echo q | gmx make_ndx -f spc216.gro >>>> echo -e "1\n1" | gmx rdf -f spc216.gro -s topol.tpr -n index.ndx >>>> -selrpos mol_com -seltype mol_com -bin 0.02 >>>> wget >>>> https://raw.githubusercontent.com/votca/csg/master/src/tools/references/spce/mapping.xml >>>> wget >>>> https://raw.githubusercontent.com/votca/csg/master/src/tools/references/spce/settings_rdf.xml >>>> csg_stat --options settings_rdf.xml --top topol.tpr --trj spc216.gro >>>> --cg mapping.xml >>>> csg_map --top topol.tpr --trj spc216.gro --cg mapping.xml --out cg.dump >>>> ``` >>>> and then calculate the rdf from cg.dump with ovito and vmd and compare >>>> them with rdf.xvg and CG-CG.dist.new. >>>> >>>> Christoph >>>> >>> >>> Ovito and VMD give nearly the same results (green X / blue square). I'm >>> not sure how those two really compute the RDF. For Ovito I can set the >>> cutoff and the number of bins (9.0, 45) and i think the bin center is on >>> the x coordinates. In VMD i can set the cutoff and the delta (9, 0.2). As >>> said, i'm not sure how the bins are decided inside those two progs, so this >>> might lead to small offsets. >>> cg_stat on the other hand is a little bit off compared to ovito and vmd. >>> But this could be imho due to the binning as mentioned before. >>> qualitatively i think it's pretty much the same. >>> >> You can pick the bins size for csg_stat in settings_rdf.xml and for gmx > on command line so you can make it same as vmd for the comparison. > > Christoph >
bin size is the same. 0.2 in vmd, 0.02 in settings_rdf.xml. I forgot the plot in the last post >>> - regards >>> Wolfgang >>> >> forgot the plot >> >>> >>> >>> >>>> >>>> >>>>> >>>>> Am Mittwoch, 8. April 2020 18:17:20 UTC+2 schrieb Christoph Junghans: >>>>>> >>>>>> >>>>>> >>>>>> On Wed, Apr 8, 2020 at 5:01 AM Wolfgang Verestek < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> Am Mittwoch, 8. April 2020 02:07:39 UTC+2 schrieb Christoph Junghans: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Apr 7, 2020 at 9:59 AM Wolfgang Verestek < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>>> Dear Christoph, >>>>>>>>> >>>>>>>>> thanks for your fast response. i followed you suggestion, renamed >>>>>>>>> the files and added the box tag to the topology file (files >>>>>>>>> attached). But >>>>>>>>> the result stays the same. So, as you said that gromacs format is >>>>>>>>> better >>>>>>>>> supported i changed my output to gro87 format. No errors, but the >>>>>>>>> discrepancy remains, regardless if i'm using wrapped or unwrapped >>>>>>>>> coords in >>>>>>>>> the conf.gro file. See below. Are there any other things i could >>>>>>>>> change? >>>>>>>>> Another format? >>>>>>>>> Is it possible to set the boundary conditions somewhere >>>>>>>>> specifically? Or could it be that periodic images of the specific >>>>>>>>> atoms are >>>>>>>>> ignored (the simulation box is kind of small and close by region >>>>>>>>> seems ok)? >>>>>>>>> >>>>>>>> Sorry, I didn't have time to look at your files yet, but does OVito >>>>>>>> handle exclusion in the same way as VOTCA? >>>>>>>> Have a look at the output of "csg_dump --top topology.xml --excl" >>>>>>>> >>>>>>> >>>>>>> How should that look like? I'm not sure if i understand that format >>>>>>> correctly, but it seems correct to me. in my data file Atom with id 1 >>>>>>> is >>>>>>> connectod to atoms 2 3 4 and 36. I assume this is non repetitive so id >>>>>>> 4 >>>>>>> does not show up again for atom id 4 and so on. I did not check the >>>>>>> whole >>>>>>> list, but the first 10 lines are correct. >>>>>>> >>>>>>> I have 164 beads in 1 molecules >>>>>>> >>>>>>> List of exclusions: >>>>>>> 1 2 3 4 36 >>>>>>> >>>>>> This means the atom #1 is excluded with atom #2, #3,#4 and #36 and >>>>>> hence contributions from these pairs won't go into the RDF. >>>>>> VOTCA automatically created exclusion (in same way as Gromacs does) >>>>>> for bonds, angles and dihedrals. >>>>>> >>>>>> Christoph >>>>>> >>>>>> >>>>>>> 4 5 6 7 >>>>>>> 7 8 9 10 >>>>>>> 10 11 12 >>>>>>> 12 13 14 >>>>>>> 14 15 16 17 >>>>>>> 17 18 19 39 >>>>>>> 20 21 22 23 77 >>>>>>> ... >>>>>>> >>>>>>> >>>>>>>> Secondly you could use "csg_map --top topology --no-map --trj >>>>>>>> lammps.dump --out out.pdb", to check if the coordinates are read >>>>>>>> correctly. >>>>>>>> >>>>>>> apart from the bigger cell for the pdb (where this information is >>>>>>> not included) the positions look ok. (lammps file in "black cores", pdb >>>>>>> in >>>>>>> transparent green). >>>>>>> >>>>>>>> >>>>>>>> Christoph >>>>>>>> >>>>>>>>> >>>>>>>>> Is there a way to visualize the xml or gro files? I know vmd, but >>>>>>>>> that segfaults when reading the gro file. >>>>>>>>> >>>>>>>>> Ultimately the whole thing should go into force matching. But i >>>>>>>>> guess the results will be off if already the RDF is wrong? >>>>>>>>> >>>>>>>>> Is it really necessary to have one file per molecule type and what >>>>>>>>> distinguishes different molecule types? If i have several PA6 >>>>>>>>> molecules >>>>>>>>> with different length/count of monomers is that already different >>>>>>>>> molecules? >>>>>>>>> >>>>>>>>> Thanks and regards >>>>>>>>> Wolfgang >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> 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 view this discussion on the web visit >>>>>>>>> https://groups.google.com/d/msgid/votca/b4b7484f-2663-4fe6-a082-ad3c2ca1ef20%40googlegroups.com >>>>>>>>> >>>>>>>>> <https://groups.google.com/d/msgid/votca/b4b7484f-2663-4fe6-a082-ad3c2ca1ef20%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>>>> . >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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 view this discussion on the web visit >>>>>>> https://groups.google.com/d/msgid/votca/3cd73547-59da-4de8-894d-0345302ebeca%40googlegroups.com >>>>>>> >>>>>>> <https://groups.google.com/d/msgid/votca/3cd73547-59da-4de8-894d-0345302ebeca%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>> . >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Christoph Junghans >>>>>> Web: http://www.compphys.de >>>>>> >>>>> -- >>>>> Join us on Slack: https://join.slack.com/t/votca/signup >>>>> --- >>>>> 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] <javascript:>. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/votca/9c1da74b-2bca-4aa5-b1a1-f26123328000%40googlegroups.com >>>>> >>>>> <https://groups.google.com/d/msgid/votca/9c1da74b-2bca-4aa5-b1a1-f26123328000%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> >>>> >>>> -- >>>> Christoph Junghans >>>> Web: http://www.compphys.de >>>> >>> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> 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] <javascript:>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/12ef52f9-854d-4404-95e5-54437779ae7a%40googlegroups.com >> >> <https://groups.google.com/d/msgid/votca/12ef52f9-854d-4404-95e5-54437779ae7a%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- > Christoph Junghans > Web: http://www.compphys.de > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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