2014-06-04 7:52 GMT-06:00 Vitalie Botan <[email protected]>: > Dear Victor, > > I am trying to coarse grain my atomistic trajectory calculated in Lammps and > follow your instructions, but the dump file saved as you suggested will: > a) have no atoms ids/types/molecular id; > b) store coordinates in angstroms (if real units were used in the atomistic > simulation) and have normally the box centered around the origin. > > Are there any setting or options to take into all these points or I have to > take care about them when exporting from Lammps? You are replying to an email, which is close to 3 years old, a lot of things have changed since then.
Concerning your questions: a.) You will need to create an xml topology to group atoms into molecules, see: <https://code.google.com/p/votca/source/browse/spce/ibi_lammps/topol.xml?repo=csg-tutorials> b.) VOTCA calculates in nm internally, but because as lammps supports too many units systems, we don't touch the units in the case of LAMMPS. Anyhow the units won't change if you convert to the same file type (e.g. dump to dump), only if you convert dump to pdb you have to be careful. b2.) VOTCA just maps the coordinates (using pbc), so a centered trajectory will be mapped to a centered coarse-grained trajectory (just like in the case of gromacs files). Christoph > > Best, > Vitalie > > On Tuesday, June 21, 2011 12:26:30 PM UTC+2, Victor Rühle wrote: >> >> Dear Sacha, >> >> it would be good to know a bit more about your system to evaluate >> which is the simplest way (how complex is your molecule on >> coarse-grained level?). You will be able to parse your lammps >> trajectories and use them as a topolgoy, but using lammps for the >> iterative process would require some modifications of the scripts. >> >> VOTCA supports reading of lammps trajectories, if you name them with >> the ending .dump. These can also be used as topologies by specifying >> an additional xml file. I tested it using the following in the lammps >> script: >> >> dump id all custom 100 system.dump x y z fx fy fz (forces are >> optional) >> >> This can be used directly as trajectory, but for a topology and >> additional file specifying the molecule information is necessary. If >> you want to use that as a topology, you'lll have to specify an >> additional xml file topol.xml where molecules and names are specified >> (in the manual is a similar example using a pdb file). >> <topology base="system.dump"> >> <molecules> >> <clear/> >> <define name="water" first="1" nbeads="3" nmols="1000"/> >> </molecules> >> </topology> >> >> then you can use e.g: >> csg_map --top topol.xml --trj system.dump --cg bla.xml ... >> >> To summarize: the missing bit is this xml file, you can use .pdb, >> .dump, .tpr as base files. Lammps can probably directly write molecule >> information. I didn't had it in my example and am not so familiar with >> lammps, so it's not implemented yet. Be aware that csg_gmxtopol will >> require some manual adjustments of the topology file. >> >> If you want to use IBI or IMC: the scripts to run lammps simulations >> are not yet implemented since we didn't use it here. One way is to run >> the iterative procedure using gromacs (which should not be hard to >> setup and i can guide you to a proper example depending on your >> coarsee-grained topology). Otherwise, if you want to use lammps for >> coarse-grained iterations (it needs to support tabulated potentials >> then), you'll have to modify a few scripts (~ 3 scripts and maybe 30 >> lines of code). >> >> Let me know which way you would prefer and we can post further details >> how to proceed. >> >> Cheers, >> Victor >> >> >> 2011/6/21 Sacha Mould <[email protected]>: >> >> >> > Hi all, >> > >> > i wonder if someone already runned votca from Lammps atomistic dump >> > files.Lammps is capable to dump .xtc trajectory file, but i'm having >> > problems to get the .tpr file in order to obtain coarsed-grained .top >> > and .gro files using csg_map and csg_gmxtopol commands. I'm interested >> > to run IBI and IMC simulations and i'm using Votca 1.1.2 release. >> > >> > I appreciate if someone can give me a tip. >> > >> > Many regards, >> > >> > >> > Sacha >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups "votca" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> >> > For more options, visit this group at >> > http://groups.google.com/group/votca?hl=en. >> > >> > > > -- > 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.
