On Thu, Apr 16, 2020 at 9:27 AM Wolfgang Verestek < [email protected]> 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 > > 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 protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/11968a7e-fb3e-443d-8af5-a2773e241335%40googlegroups.com > <https://groups.google.com/d/msgid/votca/11968a7e-fb3e-443d-8af5-a2773e241335%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Christoph Junghans 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