Simulaid: simulation setup and analysis utilites

Last updated: 07/24/2021

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Features added after the publication of the paper
Generate crystal unit cell, biological dimer from asymmetric unit
Calculate and plot the difference between residue distance matrices and residue RMSFs
Rotate a molecule based on a bond direction Calculate intermolecular distance matrix
Concatenate atom-atom bond histories to residue-residue bond histories
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 

Simulaid can perform the following operations:

List of other programs

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