SIMULATION AND ANALYSIS
AMBER - a general purpose molecular dynamics and simulation package, with many features relevant to NMR structure determination. These include time-averaged restraints, diamagnetic and paramagnetic chemical shift restraints, and "direct" refinements against NOESY volume data.
CORMA " (COmplete Relaxation Matrix Analysis) is a FORTRAN program for calculating the dipole-dipole relaxation matrix for a system of protons and converting that to intensities expected for a 2DNOE experiment." - UCSF, USA.
DSYMPC"NMR SIMULATION AND ITERATION TOOLS FOR PCs" - G. Hdgele at al., Duesseldorf, Germany.
FIRM - Full Iterative Relaxation Matrix program. "Interactive program (fortran) for calculating NOEs of a structural model using the relaxation matrix approach. Distances, corrected for the effects of spin diffusion, can be back-calculated from experimetal NOEs using a hybrid relaxation matrix. Includes features for simulating internal motions". (S. Edmondson, University of Alabama in Huntsville).
GAMMA - "a library written for simulation of Nuclear Magnetic Resonance experiments" - ref: S.A. Smith, T.O. Levante, B.H. Meier and R.R. Ernst (ETH, Switzerland); Computer Simulations in Magnetic Resonance: An Object-Oriented Programming Approach, Journal of Magnetic Resonance, November 1993, Series A. (ftp link to ETH).
MathNMR - Mathematica package for NMR spin and spatial tensor manipulations. Arbitrary spin systems, commutators, projection operators, rotations, Redfield matrix elements, matrix decomposition into basis operators, change of basis, coherence filtering, and the manipulation of Hamiltonians. The package is available for free. Alexej Jerschow, NYU.
MEX and CIFIT - Alex Bain: "For simulation of exchanged-broadened lineshapes for uncoupled spin systems (MEX) and "to analyse selective inversion experiments (Hoffman-Forsen) for slow chemical exchange (CIFIT).
MORASS - Multiple Overhauser Relaxation AnalysiS and Simulation. "MORASS uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances. MORASS analyzes 2D NMR NOESY data from oligonucleotides and proteins to evaluate cross-relaxation rates from which interproton distances are obtained" - R.P. Meadows, C.B. Post, and D.G. Gorenstein, Purdue Univ. USA.
NUMARIT- "A spin simulation/iteration package for the X32", by Kirk Marat.
PERCH - (PEak reseaRCH) - an integrated NMR-software package for research, analytics and education. The spectral analysis and simulation up to 10 spins is based on the program MLDC (Modified LAOCOON with Dipolar Couplings)" - PERCH Project, Univ. of Kuopio, FINLAND.
PJNMR - PJNMR allows visualization and simulation of up to a three spin heteronuclear or homonuclear system for pulse sequence creation.
QSim - program for simulation of liquid state NMR experiments. QSim has a graphical user interface, and pulse sequences are set up graphically. Pulse sequence elements that can be simulated include gradients, shaped pulses and decoupling sequences. Spin systems with any NMR-active nuclei can be simulated. Relaxation is included in all parts of simulations. First order chemical exchange may be included in simulations. Simulations are performed using quantum mechanical or classical mechanics. Processing may be performed in the program and 1D and 2D spectra plotted. Courtesy of Magnus Helgstrand, Dept. of Biophysical Chemistry, Lund University, Sweden
SIMMOL - Software for specification and 3D visualization of anisotropic interaction tensors from pdb-structure of peptides and proteins. The software allows straigthforward establishment of the orientations and magnitudes of anisotropic tensors for numerical simulations of peptide/protein solid-state NMR spectra using SIMPSON - Mads Bak, Robert Schultz, Thomas Vosegaard, and Niels Chr. Nielsen
SIMPSON - (SIMulation Package for SOlid-state Nmr spectroscopy) - A free solid-state NMR simulation program with emphasis on ease of use. Multiple pulses, spins, and dimensions. Flexible Tcl input files. Extended documentation for various experiments - Mads Bak, Jimmy T. Rasmussen, and Niels Chr. Nielsen, Lab. Biomol. NMR, Aarhus, Denmark.
PC Software: APT, DECAY, DEPT, FIDUNK, FTNMR Simulator, HETJ-2D, HOMOJ-2D, IRREADER, NMRSM, UNKINP, XHCORR from Dr. Harold M. Bell, Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
WINDNMR-Pro (DNMR71.EXE) is a Windows program for simulating high resolution NMR spectra. The 16-bit version of WINDNMR was published by the Journal of Chemical Education - Software. The program will run on all versions of Windows (95, 98, NT, ME, 2000, XP, Professor Hans J. Reich, Department of Chemistry, University of Wisconsin, Madison, USA.