Hi, Is there an option not to scale the output. So for example, I have a dump file which was written in LAMMPS "real" units (Angstroms, kcal/mol). I would like to map the trajectory, or write out a *pdb file, but csg-map as you state below assumes the dump file is in nm. Is there a way to tell cg-map that I do not want it to scale and use the coordinates as is,
So I could do something like csg_map --top --topol.xml --trj water_aa.dump --cg cg_water.xml --out cg.pdb --nframes 1 This would write out a cg.pdb file which I could then use with topotools to write out the LAMMPS input ".data" file. Can that be defined in the all-atom topol.xml file? Currently though csg_map is scaling everything by 10. Thanks. Josh On Saturday, February 28, 2015 at 9:37:29 AM UTC-5, Christoph Junghans wrote: > > 2015-02-27 5:17 GMT-07:00 Vitalie Botan <[email protected] <javascript:>>: > > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
