2015-02-27 5:17 GMT-07:00 Vitalie Botan <[email protected]>: > Hi, > > It seems like VOTCA has an additional factor 10 when converting between > Angstroms and nm: > the COM coors calculated from lammps dump in VMD are as they are supposed to > be in Angstroms, but the output from csg_map is 10 times larger. In the > example above the coordinates of B1 bead should be 1.6348 -13.9948 3.7050 > in Angstroms or 0.16348 -1.399 0.37 in nm, but they are multiplied by 10, > i.e. the output units are 10^-11, not 10^-9. > Of course I can scale the output manually, but I am not sure if the same > routine is used in other scripts like csg_stat or csg_boltzmann. Can you > check if the same scaling problem exists in the internal routines of other > scripts? Ok, maybe I wasn't very clear, VOTCA assumes dump files are in nm, independently if this is actually the case or not. However, this only matters if you convert between different simulation programs/formats. Example: $ csg_map --top topol.xml --out conf.dump --trj spce.dump --no-map no unit change (dump and dump have the same length unit) $ csg_map --top topol.xml --out conf.gro --trj spce.dump --no-map no unit change (gro and dump have the same length unit) $ csg_map --top topol.xml --out conf.pdb --trj spce.dump --no-map (factor 10, as dump is nm and pdb is angstrom)
That implies, one can also run an IBI iteration in units different from nm as long as one keeps using the same file format and hence no scaling is performed. Christoph > 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. -- 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 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.
