Am Freitag, 17. April 2020 15:38:05 UTC+2 schrieb Christoph Junghans: > > > > On Thu, Apr 16, 2020 at 9:27 AM Wolfgang Verestek <[email protected] > <javascript:>> wrote: > >> >> >> 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]> >>> 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? >> > Yes, for the RDF only the first image is considered. > > For force interactions it depends, Lennard-Jones usually only uses the > first image, but coulomb interactions, as they decay slower, sum over all > images (see Ewald summation). > > Christoph >
That does not sound very consistent to me. Nevertheless Thank you very much for the explanation. Altogether it already helped. Thanks Wolfgang > >> >> 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 [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. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email 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