On Thu, Apr 16, 2020 at 1:37 AM Wolfgang Verestek < [email protected]> wrote:
> > > Am Mittwoch, 15. April 2020 14:55:59 UTC+2 schrieb Christoph Junghans: >> >> >> >> 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. >> > ok, thanks. But could give me a hint why such a cutoff is physically not > meaningful? I understand that such a small system does have bad statistics > etc. but the particle is not self-interacting (although the molecule is, > but it's also doing that with cutoff of 0.5* box length). Isn't that > exactly what periodic boundaries should cover? I mean, extreme case here, > but...? > Periodic boundaries follow minimum image convention, that means one only counts minimum of all distances in all periodic images. Imagine a 1D box of length L and put one particle at 0 and another at L/2. Their distance will be L/2, but if you move it further away from 0, it will come closer to the periodic image of the 1st particle sitting at L and hence making the distance shorter again. In 3D there is another factor of sqrt(3), but I think that is the reason why VMD had 0s in the rdf for bigger distances. Christoph > > >> >> 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. > 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/6152ba41-02d8-4400-ade4-1f1b2e27f13d%40googlegroups.com > <https://groups.google.com/d/msgid/votca/6152ba41-02d8-4400-ade4-1f1b2e27f13d%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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