This fix seems to be very useful and I want to try it with the new version
of LAMMPS. However, I have no experience in using VMD and it says in the
manual that this fix needs to have a topology or coordinate file that has
to be loaded in VMD. Does anyone know what the format is for this
topology/coordinate file? I intend to just print this file out together
that can be almost anything that VMD can handle. the important issue
is that it has to match the group that you want to apply the fix to.
e.g., if you have a solvated molecule and only want to apply IMD to
the molecule, but not the solvent.
via the topotools plugin, most data files can be read in, too,
but usually a .psf/.pdb file combination is more convenient to
use, as one can assign text labels to atom types/names molecules,
with the data file for my LAMMPS simulations. How different is the format
of this topology/coordinate file from a LAMMPS data file?
VMD supports a large number of file formats. only some of them
store topology information. the IMD instructions on the VMD homepage
focus on hooking up NAMD with VMD, and there the combination of
.psf/.pdb is quite common.
i will send you a set of demo inputs in a separate e-mail, which
is for a deca-alanin helix solvated in water with the two variants
i mentioned and a modified version of the "melt" example. this
file is 0.5MB, so i don't want to needlessly flood other people's
mailboxes with something that they may not care so much about.
if there are more people interested, i can upload them somewhere
on the web...
btw: the real fun starts when you can use something else then
just a mouse to apply the force (that interface was supposedly
an afterthought and is a bit clunky). i have some hacks (adapted
from code that a friend wrote) in my personal VMD version where
i can use a WiiMote controller, which is pretty neat.
cheers and good luck,