Thanks. I think VMD does the same thing you do. It interprets the *.gro file as in nm, so if it converts it to say *pdb, it also would multiply by 10.
I'm trying to get Votca to work with LAMMPS in "real" units, all the way through from atomistic trajectory all the way through ibi. On Saturday, February 11, 2017 at 7:03:58 PM UTC-5, Christoph Junghans wrote: > > 2017-02-11 16:36 GMT-07:00 Joshua Moore <jdm...@ncsu.edu <javascript:>>: > > 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. > Sorry, even though adding a scale option to the topology class isn't > hard, no improvements has been made on that front (pull requests > welcome). > > As a workaround, I think, topotools supports the gro file format as > well, which is in nm, and hence won't have any scaling difference when > converting from a dump file using csg_map. > > Christoph > > > > 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 <vitali...@gmail.com>: > >> > 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 votca+un...@googlegroups.com. > >> > To post to this group, send email to vo...@googlegroups.com. > >> > 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 votca+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <javascript:>. > > Visit this group at https://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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
