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 > > >> >> 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/89f1893d-8ac7-4325-907e-91ecfba27432%40googlegroups.com.
