2014-09-21 16:08 GMT-06:00 Christoph Junghans <[email protected]>: > 2014-09-21 8:53 GMT-06:00 Sikandar Mashayak <[email protected]>: >> Hi, >> >> I am trying to set up a coarse-graining simulation with LAMMPS as a >> simulation program. However, I am not quite sure how to specify the mapping >> and topology info. In the spce/ibi_lammps example, there is a topol.xml file >> for CG topology, but its structure is not clear to me, especially terms like >> topology base and first. Also, can anyone give me an example of mapping >> using LAMMPS trajectory files? > topol.xml looks like: > <topology base="spce.dump"> > <molecules> > <clear/> > <define name="SOL" first="1" nbeads="1" nmols="2180"/> > </molecules> > </topology> > The base="spce.dump" means read "spce.dump" and setup topology > information like given therein. > In the case of a dump file, VOTCA reads the atom types (an integer, > hence type1="1" in settings.xml), positions and the box size, all in > lammps units. > For other file formats like gro, xyz or pdb as base, things might be > different as some of them don't have box sizes. > > The dump file contains no information about which atoms belong to > which molecule. > For that > <clear/> > <define name="SOL" first="1" nbeads="1" nmols="2180"/> > is used. <clear/> removed all molecule read (in case of a dump file > none), but it don't hurt to do it. > Then we setup 2180(=nmols) molecules with 1(=nbeads) bead each > starting from atom "1"(=first). > That is it. For more complicated system you can have multiple of these lines. > > You don't need to use a dump file as a topology base, a pdb will do, too. > But for a pdb you will need to set the box using a line like > <box xx="4.03100" yy="4.03100" zz="4.03100"/> > inside the <topology> block.
Sorry I forgot to say in the same way you can build a topology for an atomistic trajectory. Most likely you will also need to use the rename tag <rename name="NewName" range="1:1:10"> (range=min:step:max) to give the molecule the right name. Christoph > > Christoph >> >> Thanks, >> Sikandar >> >> -- >> 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 -- 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.
