Dear Christoph, Thank you for your reply.
I have figured out the solution. Actually, the format of the LAMMPS topology file was not in alignment with the VOTCA topology.xml file. So, I have changed the order in the LAMMPS topology file so that it matches with the VOTCA topology.xml file. Now, its working and I am able to generate my RDF. Thank you. Sanjeet On Tuesday, February 28, 2023 at 10:32:40 PM UTC-5 Christoph Junghans wrote: > On Mon, Feb 27, 2023 at 8:23 PM Sanjeet Singh <[email protected]> wrote: > >> Dear Christoph, >> >> Thank you for your prompt response. >> >> Sorry, I didn't convey my points clearly. I want to say that atom with id >> 766 is a single atom cation. In CG representation, it is a bead consisting >> of only one atom. While atom with id 780 is an atom belonging to an anion >> consisting of 15 atoms. Below I have attached the details from the LAMMPS >> trajectory file. >> >> id mol type q x y >> z fx fy fz >> >> 766 12 7 1 1.29656 21.7926 >> 13.5263 -0.34422 0.0733004 -0.408895 >> >> 780 13 5 -0.118 15.8523 12.1644 >> 1.58685 -0.908541 2.12485 -4.0017 >> >> So, atoms with id 766 and 780 are not part of a single bead. In fact, >> they are not part of the same molecule. Therefore, there is no point in >> checking the condition "coarse-grained bead is bigger than half the box". >> >> Actually, my system consists of 10 polymer chains and 7 ion pairs. So, I >> have three types of molecules in my system: first polymer, second anion, >> and third cation. And, in the LAMMPS data file the atoms are listed such >> that first, it gives the coordinates of the atoms of the 10 polymer chains, >> followed by the coordinates of the first anion and cation, then the >> coordinates of the second anion and cation, and so on. >> >> But, csg_stat is reading the trajectory in such a way that the LAMMPS >> data file first lists the coordinates of the 10 polymer chains, followed by >> the coordinates of the 7 anions in my system, and then the 7 cations, which >> is not the correct order. >> > Sorry isn't that the order how you list it in your topology.xml? You can > run "csg_dump --top topology.xml" to see the order VOTCA is expecting. > The actual order in the dump file doesn't matter, VOTCA reads the atom id > and then stores it in the right spot, you can test that by doing a dummy > mapping (csg_map --no-map --trj file.dump --out file.xyz) > > Christoph > > >> >> I have also verified this using the csg_dump command. I have also >> rechecked my mapping and topology files, I didn't find any mistakes in >> these files. >> >> Can you please suggest to me how to correct this? Maybe a possible >> workaround for this? >> >> Thank you. >> >> Sanjeet >> >> On Mon, Feb 27, 2023 at 4:30 PM Christoph Junghans <[email protected]> >> wrote: >> >>> >>> >>> On Sun, Feb 26, 2023 at 11:38 Sanjeet Singh <[email protected]> wrote: >>> >>>> Hello Everyone, >>>> >>>> I am trying to generate RDF for a Homopolymer electrolyte system using >>>> csg_stat command as below: >>>> >>>> csg_stat --top topology.xml --trj Trajectory2.dump --cg >>>> "PL.xml;SI.xml;L.xml" --options NONBON-RDF.xml >>>> >>>> But, I am getting the below error: >>>> >>>> Reading frame, timestep 0 >>>> 0.129656 >>>> 2.17926 >>>> 1.35263 1.58523 >>>> 1.21644 >>>> 0.158685 >>>> an error occurred: >>>> coarse-grained bead is bigger than half the box >>>> (atoms CT1 (id 766), FT15 (id 780), molecule 12) >>>> >>>> From the above message, it can be seen that the error occurred at >>>> timestep 0. So, I tried to verify the error. The coordinates of the atoms >>>> with id 766 and id 780 are read correctly from the trajectory file. But, >>>> atom CT1 and FT15 belong to molecule 13, and not 12. CT1 should be >>>> actually >>>> LI1 as per my topology. >>>> >>> 12 vs 13 is C numbering that starts with 0, so 0, 1, 2. >>> >>> How big is your box and is any of the 3 distances in x,y or z bigger >>> than half of that? >>> >>> Usually this error hints at an error in the mapping, but if you are 100% >>> sure, that is right but increase the box size. >>> >>> Christoph >>> >>> >>>> Actually, my system consists of 10 polymer chains and 7 ion pairs. So, >>>> I have three types of molecules in my system: first polymer, second anion, >>>> and third cation. And, in the LAMMPS data file the atoms are listed such >>>> that first it gives the coordinates of the atoms of the 10 polymer chains, >>>> followed by the coordinates of the first anion and cation, then the >>>> coordinates of the second anion and cation, and so on. >>>> >>>> But, csg_stat is reading the trajectory in such a way that the LAMMPS >>>> data file first lists the coordinates of the 10 polymer chains, followed >>>> by >>>> the coordinates of the 7 anions in my system, and then the 7 cations, >>>> which >>>> is not the correct order. >>>> >>>> I have also verified this using csg_dump command. >>>> >>>> Can you please suggest to me how to correct this? Maybe a possible >>>> workaround for this? >>>> >>>> Please find attached my topology, and mapping file. >>>> >>>> Thank you. >>>> >>>> Sanjeet >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> 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/f7627abb-56c9-45e8-b614-6576eac1c22bn%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/votca/f7627abb-56c9-45e8-b614-6576eac1c22bn%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/CAHG27e6PmSja%2BogTKs0CujXvptnC_uaq2tC%3D2uMpcTqSwMJDVA%40mail.gmail.com >>> >>> <https://groups.google.com/d/msgid/votca/CAHG27e6PmSja%2BogTKs0CujXvptnC_uaq2tC%3D2uMpcTqSwMJDVA%40mail.gmail.com?utm_medium=email&utm_source=footer> >>> . >>> >> >> >> -- >> *Sanjeet Kumar Singh* >> >> *Postdoctoral Fellow* >> >> *LPCM Lab.* >> *University De Sherbrooke* >> *Sherbrooke, Canada.* >> >> -- >> 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/CABgeOedaHFsZuRNmf7kbs9NgjH_g7vTMz9SMOwmQM0SeD0%2BrJQ%40mail.gmail.com >> >> <https://groups.google.com/d/msgid/votca/CABgeOedaHFsZuRNmf7kbs9NgjH_g7vTMz9SMOwmQM0SeD0%2BrJQ%40mail.gmail.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. 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