On Wed, Apr 15, 2020 at 05:56 Wolfgang Verestek <[email protected]> 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 > >> - 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. > 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/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. 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/CAHG27e759Xd8QukX6U%2BNBOW-QHh-ZH_cjf9JJ-o76WNHnShKaA%40mail.gmail.com.
