lammps/examples/USER/imda2ea5509ff14efficient_neuronet
imd
README
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 -log none -in in.melt_imd & vmd -e melt_imd-demo.vmd
When exiting VMD, the simulation will either continue or wait for a new connection depending on whether the "nowait" flag was activated or not. To terminate the LAMMPS simulation, type "imd kill" into the VMD command line prompt.
To combine interactive MD with force feedback using a Novint Falcon game controller, have a look at: http://sites.google.com/site/akohlmey/software/vrpn-icms
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.
bucky-plus-cnt:
this is "the buckyball challenge". a demo that is very popular to demonstrate the use of IMD with force feedback. The system is a SWCNT with some atoms fixed in space and five C60 fullerenes in a reflecting wall box. The challenge is to push all five buckyballs into the nanotube and have them stay inside.
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 <akohlmey@gmail.com>.