Steve, LAMMPS users,
After running LAMMPS simulations on a single processor, I have been
able to load a dump file from LAMMPS into VMD (as LAMMPS trajectory
file) and view the animations without problems. However, after I run
the LAMMPS simulation on multiple processors, there are errors with
reading the dump file into VMD.
please tell us what the errors _are_?
there is no principle problem in VMD with reading
trajectory files from parallel runs. the difference
has to be elsewhere.
please note that the LAMMPS dump file format had some
changes recently, and those break the LAMMPS trajectory
reader in VMD 1.8.6. this has been corrected and the
LAMMPS reader in VMD greatly enhanced. the latest beta
version for VMD 1.8.7 has all those changes included.
As an alternative, I was advised to try the dcd format for outputting
the coordinates from LAMMPS; however, I believe a structure file
(psf?) is required to be input in VMD prior to loading the dcd file. I
was unsure of how to create this structure (psf) file within the
framework of LAMMPS.
.dcd files only contain coordinates, so they have no
information about atom types, bond and so on. in CHARMM
(and NAMD) the .psf file more-or-less is the equivalent
of the data file in LAMMPS and thus contains the missing
information (data files in LAMMPS can contain more data).
again, in this case you would benefit a lot from trying
out the latest VMD-1.8.7 beta. this contains a package
called topotools, that can read quite a few variants of
LAMMPS data files and thus can be used to create a .psf
file or to load a .dcd file on topo of it.
this has to be done from the VMD command terminal window:
package require topotools
topo readlammpsdata data.file atom_style
(please replace data.file with your data file name
and atom_style with the atom style used).
mol addfile file.dcd waitfor all
(to load a .dcd on top of it)
or to save a .psf you can do (with or without the .dcd):
animate write psf file.psf
if you have some files that don't work with the
last VMD beta, i would be _very_ interested in
getting a copy of those, so the code in VMD can
be fixed before the release.