59 lines
2.3 KiB
Plaintext
59 lines
2.3 KiB
Plaintext
Interactive MD example files using the fix imd command
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To run the demos, first start the LAMMPS simulation, during
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initialization it will stop and wait for an IMD client to
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connect. Then launch VMD on the same machine with the respective
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script to connect and visualize the running simulation. For example:
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mpirun -np 4 lmp_linux -log none -in in.melt_imd &
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vmd -e melt_imd-demo.vmd
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When exiting VMD, the simulation will either continue or wait
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for a new connection depending on whether the "nowait" flag was
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activated or not. To terminate the LAMMPS simulation,
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type "imd kill" into the VMD command line prompt.
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To combine interactive MD with force feedback using a
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Novint Falcon game controller, have a look at:
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http://sites.google.com/site/akohlmey/software/vrpn-icms
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Examples:
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melt:
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an adapted version of the 3d-LJ melt example.
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the VMD visualization contains one highlighted
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atom to play with force application through a
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mouse: Open the Graphical Representations dialog,
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Double-click on the first VDW representation
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to disable it, click with the mouse on the blue
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atom and - while holding the mouse button down -
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drag the atom into some direction. A red arrow
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should appear indicating direction and magnitude
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of the force. Now double-click on the first VDW
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representation again to re-enable the rest of
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the atoms and watch the blue atom move.
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bucky-plus-cnt:
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this is "the buckyball challenge". a demo that
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is very popular to demonstrate the use of IMD
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with force feedback. The system is a SWCNT with
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some atoms fixed in space and five C60 fullerenes
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in a reflecting wall box. The challenge is to
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push all five buckyballs into the nanotube and
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have them stay inside.
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deca-ala-solv:
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a solvated deca alanin helix. The mouse mode is
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preset to move residues instead of individual
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atoms. Disable the water rep and grab an atom
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from the peptide and drag it to apply forces.
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deca-ala:
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this is the same system as the previous, but
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the fix is only applied to the peptide and thus
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the corresponding VMD script needs a different
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topology file with the matching number of atoms
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to visualize it and receive the IMD data.
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In case of problems, contact <akohlmey@gmail.com>.
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