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 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] > <javascript:>> 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] <javascript:>. >> 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. 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