Dear All,
I want to make different representations for different molecules/residues (of a system containing different proteins) in vmd. I have problem with saving information regarding molecule types (as mentioned for proteins by residue name, type etc in pdb format ) dumped in to lammps trajectory. Please suggest how can it be done?
Dear All,
I want to make different representations for different
molecules/residues (of a system containing different proteins) in vmd. I
have problem with saving information regarding molecule types (as mentioned
for proteins by residue name, type etc in pdb format ) dumped in to lammps
trajectory. Please suggest how can it be done?
you cannot and you don't have to.
please have a closer look how VMD is used with other
MD codes, e.g. NAMD or CHARMM. there you typically
have a .psf file and multiple .dcd files to represent a
trajectory. the .dcd files *only* contain coordinates
(and optionally cell dimensions). lammps can produce
the same. now all you need is a suitable .psf file or
something equivalent providing the information about
atoms and residues that you are looking for,
and you have to have something along those lines
in order to create a lammps data file in the first place.
for as long as you have the same number of atoms in
the same order (when sorted by atom id, that is) it
will work file. VMD will not read anything but the
position (and velocity) information from any file loaded
subsequently on top of the initial file.
if needed, you can even create a suitable file with some
scripting yourself. after all, it only needs to be suitable
for visualization, not for simulation.
in conclusion, this is much more of a VMD than LAMMPS
problem and an issue of not fully realizing how VMD works.
i suggest you have a closer look at the VMD user's guide
and spend some (more) time working through the VMD
tutorials. it will be worth it.
axel.