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/CAHG27e41dKaN%2BJrQhCb1vj2QUi74kEhTcRr05HASRW74%3DpUG2Q%40mail.gmail.com.
