the RDF files if you want to check yourself 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] > <javascript:>> 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] <javascript:>. >> 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 >
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CG-CG.dist.new.vmd
Description: chemical/vmd
# Radial distribution function: # "Pair separation distance" g(r) 0.1 0.0 0.3 0.0 0.5 0.0 0.7 0.0 0.9 0.0 1.1 0.0 1.3 0.0 1.5 0.0 1.7 0.0 1.9 0.0 2.1 0.0 2.3 0.0 2.5 0.2817552711 2.7 2.4459782893 2.9 1.8455026073 3.1 1.0882113475 3.3 0.8895810549 3.5 0.8986889428 3.7 0.9087259069 3.9 0.9265081308 4.1 1.0544735709 4.3 1.0718177716 4.5 1.1744131001 4.7 1.0317458881 4.9 1.1097536008 5.1 0.9651670506 5.3 0.8976268946 5.5 0.9390962791 5.7 0.9116364064 5.9 0.9078203935 6.1 0.973556075 6.3 0.9654400678 6.5 1.0581048476 6.7 1.0326755369 6.9 1.0083737899 7.1 1.0659529954 7.3 1.1075301331 7.5 0.9866109262 7.7 0.9360268715 7.9 0.9880394735 8.1 0.9868448311 8.3 1.0245767055 8.5 0.9875992798 8.7 0.9572644021 8.9 1.0092574828 9.1 0.9560756795 9.3 1.0032455204 9.5 1.0614991438 9.7 1.0392445557 9.9 1.0414974743 10.1 0.9639581213 10.3 0.9331151558 10.5 1.0487240239 10.7 0.9521790929 10.9 0.9787288365 11.1 0.9705898932 11.3 1.0132889085 11.5 1.0416320377 11.7 1.0352849354 11.9 1.0116651682 12.1 0.978498839 12.3 1.0153553522 12.5 0.9908768365 12.7 1.0111190378 12.9 0.9800101755 13.1 0.9965155388 13.3 0.9960294125 13.5 0.9745913076 13.7 0.9838929794 13.9 1.0025184932 14.1 1.0235760283 14.3 1.0349941032 14.5 1.000354946 14.7 0.9865693762 14.9 0.9895266357
CG-CG.dist.new
Description: Binary data
