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Interactive MD example files using the fix imd command
To run the demos, first start the LAMMPS simulation, during
initialization it will stop and wait for an IMD client to
connect. Then launch VMD on the same machine with the respective
script to connect and visualize the running simulation. For example:
mpirun -np 4 lmp_linux -in in.melt_imd
vmd -e melt_imd-demo.vmd
When exiting VMD, the simulation will wait for a new connection. To
terminate the LAMMPS simulation, type "imd kill" into the VMD command
line prompt.
Examples:
melt:
an adapted version of the 3d-LJ melt example.
the VMD visualization contains one highlighted
atom to play with force application through a
mouse: Open the Graphical Representations dialog,
Double-click on the first VDW representation
to disable it, click with the mouse on the blue
atom and - while holding the mouse button down -
drag the atom into some direction. A red arrow
should appear indicating direction and magnitude
of the force. Now double-click on the first VDW
representation again to re-enable the rest of
the atoms and watch the blue atom move.
deca-ala-solv:
a solvated deca alanin helix. The mouse mode is
preset to move residues instead of individual
atoms. Disable the water rep and grab an atom
from the peptide and drag it to apply forces.
deca-ala:
this is the same system as the previous, but
the fix is only applied to the peptide and thus
the corresponding vmd script needs a different
topology file with the matching number of atoms
to visualize it and receive the IMD data.
In case of problems, contact <axel.kohlmeyer@temple.edu>.
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