|From:||Stephan Grein <stephan.grein@...5733...>|
|Date:||Tue, 19 Sep 2017 19:08:50 +0200|
Am 15/09/17 um 20:56 schrieb Axel Kohlmeyer: > > > On Fri, Sep 15, 2017 at 1:48 PM, Stephan Grein > <stephan.grein@...5733... > <mailto:stephan.grein@...5733...>> wrote: > > > > > 3) create_atoms can create/distribute > > random atoms. I need however to create > > small molecules and distribute them > > randomly. The small molecule structure > > is known a-priori, however I need to > > insert let's say 10 randomly in my > > simulation box. > > > > > > with a recent enough version of LAMMPS, create_atoms can also create > > molecules that have been previously defined with the molecule command > > and read from a suitable file. > > Follow up on this: > If I would add a new ion type to my system, > I would have to specify obviously all the > interactions with the other types in my system. > Correct? So would it be better to prepare the > ion in a let's say dummy PDB file and convert > it to a LAMMPS input data with e.g. topotools > and then use read_data? > > > the read_data command takes options like: extra/atom/types > where you can reserve space for these atom types. > > the basic rules in LAMMPS related to this are simple: > - number of atom/bond/angle/dihedral/improper types per atom, max > bonds/angles/dihedrals/impropers per atom, max special per atom are > locked in, when the simulation cell is created. this happens with either > create_box, read_data or read_restart. > - this cannot be changed after that as it would require to redo the box > creation. a new box can only be created after the clear command, which > reinstantiates the LAMMPS class from scratch. > > no need to use a dummy atom, tho. Thanks for pointing that out. This might seem like a silly question: If I don't need extra atom types for my molecule I want to add via the molecule command I could just use the atom types provided from my "main molecule" which I loaded before with the read_data command. There is probably no automation I could make use of. Correct? (Just want to make sure I don't miss something or do unneccesary work). TIA. Best wishes, Stephan > > > axel. > > > > > Best regards, > Stephan > > > > > > axel > > > > > > > > > > Thanks in advance. > > > > Best regards, > > Stephan > > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > > lammps-users mailing list > > email@example.com > <mailto:firstname.lastname@example.org> > > <mailto:email@example.com > <mailto:firstname.lastname@example.org>> > > https://lists.sourceforge.net/lists/listinfo/lammps-users > <https://lists.sourceforge.net/lists/listinfo/lammps-users> > > > > > > > > > > -- > > Dr. Axel Kohlmeyer akohlmey@...24... <mailto:akohlmey@...29....> > <mailto:akohlmey@...24... <mailto:akohlmey@...24...>> > > http://goo.gl/1wk0 > > College of Science & Technology, Temple University, Philadelphia PA, USA > > International Centre for Theoretical Physics, Trieste. Italy. > > -- > Stephan Grein > Department of Mathematics > Temple University > 1805 N Broad Street, Room 513 > Philadelphia, PA 19122-6094, USA > https://math.temple.edu/~queisser/ <https://math.temple.edu/~queisser/> > phone: +1 (215) 434-5843 > > > > > -- > Dr. Axel Kohlmeyer akohlmey@...24... <mailto:akohlmey@...24...> > http://goo.gl/1wk0 > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste. Italy.
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