Am Donnerstag, 16. April 2020 16:38:40 UTC+2 schrieb Christoph Junghans: > > > > On Thu, Apr 16, 2020 at 1:37 AM Wolfgang Verestek <[email protected] > <javascript:>> 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 > Thanks for the explanation. I was not aware that every particle is considered just once.
I might be wrong, but from my understanding two interactions in the periodic 1D case would be possible. E.g. for two particles "x" and "o" with periodic boundary "|": o would have one interactions with x for d<L/2 and a second one for 0.5L<d<L, the first at 2 units distance in positive/right direction and the second with at 7 units distance in negative/left direction. So if I understand you correct, only one image of the particle with the minimum distance is considered and all the other periodic images are neglected? Image -1 | 0 | 1 Dist 98765 432101234 56789 Sys ....o.x..|....o.x..|....o.x.. Wolfgang > >> >>> >>> 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 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