Simulaid: a simulation facilitator and analysis program. Abstract: Simulaid performs a large number of simulation-related tasks: interconversion and modification of structure and trajectory files, optimization of orientation, and a large variety of analysis functions. The program can handle structures in PDB, Charmm CRD, Amber, Macromodel, Gromos/Gromacs, InsightII, Grasp .crg, Tripos .mol2 (input only) and in the MMC9 formats; and trajectories in the formats of Charmm, Amber, Macromodel and MMC. Analysis features include (but are not limited to): 1. simple distance calculations and hydrogen-bond analysis; 2. calculation of 2-D RMSD maps (produced both as text file with the data and as a color-coded matrix) and cross RMSD maps between trajectories; 3. clustering based on RMSD maps; 4. analysis of torsion angles, Ramachandran angles, proline kink angles, pseudorotational angles; and 5. analysis based on circular variance. Torsion angle evolutions are presented in dial plots. Several of these features are unique to Simulaid.