2017-02-11 16:36 GMT-07:00 Joshua Moore <[email protected]>: > 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 <[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 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 [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.
