- Fast long range electrostatics and nonbonded terms. AMMP runs without cutoffs in times comparable to or better than an 8 Angstrom cutoff in other programs.
- Stable, numerically accurate, molecular dynamics. AMMP is stable with difficult problems such as parallel stranded DNA. (shown with its Na counterions below).
- Flexible choice of potential functions. In addition to standard formulations, AMMP has non-point charges, explicit Debye screening, accurate polarization models, non-harmonic bond and angle formulations, and coupled bond-angle terms available.
- Calculates partial charges for new molecules
- Embeding and homotopy methods for rapid model building.
- Self-contained, and can be embeded in other programs
- Highly parallel version available with PVM
- Literature citations for AMMP
- Quality of the AMMP sp4 potential set
- Quality of the AMMP sp5 potential set
- Nifty windows tricks with AMMP
Data for small molecules can be found at NIST. Thermochemical and IR spectral data are used for checking the classical force field in AMMP.
Conservation of structure during long molecular dynamics
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| HIV protease Crystal Structure | HIV protease average over 590 ps |
AMMP with the sp4 potential set conserves structure. The average structure for a model of the HIV protease complex with Indanovir has essentially the same structure as the crystal structure. The calculation was performed with constant pressure/temperature dynamics on 9582 atoms without cutoff's. The linux version of AMMP was used on a pentium II 300 mhz machine and required 45 cpu minutes per ps. The total elapsed time was a little over two weeks.
