Simulation of NaCl with an MDGRAPE-2 board. The playback speed is almost the same as that you simulate with an MDGRAPE-2 board in real-time.
| System | NaCl |
| Number of atoms | 1000-1027 |
| Boundary condition | Reflect at the wall |
| Potential | Tosi-Fumi potential |
| Temperature | 300K-7200K |
| Ensenble | NVT |
| MD code | By Dr. Koishi |
| Time step | 2.0 fs |
| Total simulation time | 35 ps |
Folding simulation of a small peptide is performed from a straight string. Folding has partially done.
| System | Peptide (16 amino acid residues) |
| Number of atoms | Peptide(202)+water(25667)=25869 |
| SHAKE | All bond length were constrained |
| Boundary condition | Free |
| Temperature | 300K |
| Ensenble | NVT |
| MD code | AMBER 5.0 modified for MDGRAPE-2 |
| Time step | 1.0 fs |
| Totoal simulation time | 2.0 ns |
Mutant (G12V) of RAS p21 G-protein has an unstable atom positions at active sight. This causes the loss of function of this protein. In the movie, right one is mutant and left one is normal protein. Red atoms in the circle in the right protein are unstable than those of left protein.
DNA double helix structure is simulated. After simulation, DNA bends a little, which is the natural state.
