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.
