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. 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 -- 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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