On Wed, Apr 15, 2020 at 6:55 AM Christoph Junghans <[email protected]> wrote:
> > > On Wed, Apr 15, 2020 at 6:36 AM Wolfgang Verestek < > [email protected]> wrote: > >> There is indeed a slight difference. but as stated before, i think >> qualitatively they are matching. >> >> Second thing: I increased the cutoff to be more than half the box (9 -> >> 15 A). This results in the behavior that we have seen before. Also the VMD >> > Ok, now I see, well the box size is 18.6 A, a cutoff of more than 9.3 A > isn't really physically meaningful and csg_stat should basically warn of > that. > https://github.com/votca/csg/pull/512 > > Christoph > >> >> >> Am Mittwoch, 15. April 2020 14:13:30 UTC+2 schrieb Christoph Junghans: >>> >>> >>> >>> On Wed, Apr 15, 2020 at 6:05 AM Wolfgang Verestek <[email protected]> >>> wrote: >>> >>>> >>>> >>>> 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]> >>>>> 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 >>>> >>> Hmm, but it seems the dots are not at the same r values, or am I seeing >>> this wrong? >>> >>> 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/56cd974d-7a71-470f-b895-d95163c22596%40googlegroups.com >>>> <https://groups.google.com/d/msgid/votca/56cd974d-7a71-470f-b895-d95163c22596%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/6a39277e-ab3a-4e14-9a8b-831a1ddb24d1%40googlegroups.com >> <https://groups.google.com/d/msgid/votca/6a39277e-ab3a-4e14-9a8b-831a1ddb24d1%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- 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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