Dear Christoph, I've just realized that the newest development version of csg_map (version 1.3-dev hgid: 78c98aa45ba2) produces quite odd results when reading Lammps dump files:
when I write the trajectory in wrapped coors, i.e. ITEM: TIMESTEP 50000 ITEM: NUMBER OF ATOMS 576 ITEM: BOX BOUNDS pp pp pp -16.6546 16.6546 -16.6546 16.6546 -16.6546 16.6546 *ITEM: ATOMS id mol type x y z* 1 1 1 1.48239 -14.3129 4.66771 2 1 1 1.10847 -12.8235 4.62104 3 1 2 1.98531 -12.2345 4.39821 4 1 2 0.408144 -12.8184 3.77732 5 1 2 2.11519 -14.4292 5.57303 6 1 3 2.26613 -14.6418 3.36911 7 1 4 1.76513 -14.4093 2.27462 the coordinates of the bead corresponding to these 7 atoms as written by csg_map are: *ATOM 2 B1 UNL 1 16.348 -139.948 37.050* As you see there is a factor of 10 at least in the COM coordinates. I've check it with scaled coordinates dump: ITEM: TIMESTEP 50000 ITEM: NUMBER OF ATOMS 576 ITEM: BOX BOUNDS pp pp pp -16.6546 16.6546 -16.6546 16.6546 -16.6546 16.6546 *ITEM: ATOMS id mol type xs ys zs* 1 1 1 0.544504 0.0703018 0.640133 2 1 1 0.533278 0.115015 0.638732 3 1 2 0.559603 0.132698 0.632042 4 1 2 0.512253 0.115167 0.613402 5 1 2 0.563502 0.0668092 0.667313 6 1 3 0.568033 0.0604275 0.601147 7 1 4 0.552992 0.067407 0.568288 and it looks even worse in this case: *ATOM 2 B1 UNL 1 182.893 26.598 203.596* The only meaningful output I found for unwrapped coordinates: ITEM: TIMESTEP 50000 ITEM: NUMBER OF ATOMS 576 ITEM: BOX BOUNDS pp pp pp -16.6546 16.6546 -16.6546 16.6546 -16.6546 16.6546 *ITEM: ATOMS id mol type xu yu zu * 1 1 1 34.7915 18.9962 4.66771 2 1 1 34.4176 20.4856 4.62104 3 1 2 35.2944 21.0746 4.39821 4 1 2 33.7173 20.4907 3.77732 5 1 2 35.4243 18.8799 5.57303 6 1 3 35.5752 18.6673 3.36911 7 1 4 35.0742 18.8998 2.27462 with csg_map output *ATOM 2 B1 UNL 1 33.906 21.495 7.762* I am quite sure that the version from Nov 2014 had no problems with Lammps dumps in wrapped coordinates (I have even visualized it VMD drawing atomistic and cg trajectories over each other), so it should be a recent change in the source code. Is it an angstrom/nm convention issue or something else? If you need I can provide xml and pdb files for a single snapshot. Best, Vitalie -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
