Simulaid: simulation setup and analysis utilites

Last updated: 07/29/2022
M. Mezei, J. Comp. Chem., 31, 2658-2668 (2010). DOI:10.1002/jcc.21551

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Features added after the publication of the paper
Generate crystal unit cell, biological dimer from asymmetric unit
Cluster and subcluster based on input data (e.g., Tanimoto similarity matrix)
Separate a GCE trajectory into Amber trajectories Extract cluster center structures after clustering
Read charges from Charmm or Amber topology file or Autodock .pdbqt file
Calculate and plot the difference between residue distance matrices and residue RMSFs
Calculate and plot the difference between bond (hydrogen/hydrophobic bond; salt bridge) matrices
Individualize atom names, scale coordinates, save mol2 file with names or coordinates changed
Allow atom selection by atom or residue names; generate plot of atom-atom distance SDs
Support for Tripos .mol2 (mostly for input) and Maestro .mae (only for input) formats
Rotate a molecule based on a bond direction Calculate intermolecular distance matrix
Concatenate atom-atom bond histories to residue-residue bond histories
Calculate bond state statistics and autocorrelations Draw bonds between (anti)correlated bonds
Heuristic clustering into cliques Density-based clusterings
Helix analysis (TRAJHELIX) on several helices Filter solvents by proximity, CV or interface
Align a molecule's principal axes to the XYZ axes Calculate angle distributions with dial plots
Calculate two kinds of helix-helix distances, and helix rotations relative to other helices
Filter for solvents forming H-bond bridges Bond tracks for mutually proximal atom pairs
Residue-residue autocorrelation (lifetime) Swap chirality
Input of PDBx/mmCIF files Convert sequence files
Read bond list from RTF or top files; print MMC MAKB or PDB CONECT records
Specify atom lists for molecular overlay Filter trajectories/structures for energy
Plot and cluster torsion angle circular correlation matrix, calculate its eigenvectors, eigenvalues
Create a PDB file of a rectangle (box/cube) Calculate RMSD for residues
Process clusters with user-defined limits; use even-spaced or random intial trys for clustering
Create periodic replica cells Plot PBC cell sizes, volume
Track solvent diffusion, membrane transit Principal axes by domains, angle between them
Average data in 1D plots Calculate membrane deviation from flatness
Inertia plot for K-means and K-medoid clustering  

Simulaid can perform the following operations:

List of other programs

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