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. > > - 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]. >>> 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. 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