Program for Analysis of Internal Motion in Molecular Dynamics Simulation
| Authors | |
|---|---|
| Year of publication | 2007 |
| Type | Article in Proceedings |
| Conference | Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul" |
| MU Faculty or unit | |
| Citation | |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | MD; PAIN; protein; dynamics; |
| Description | Molecular dynamics (MD) simulations of the proteins provide us huge amount of data describing coordinates of all atoms and their changes in course of time. This enables us to extract motional parameters of the studied molecule. For this purpose the program PAIN (Program for Analysis of Internal motioN) was written. It is written in C language so that the analysis of large amount of data is fairly fast and it should be rather easily portable on the majority of the current platforms. Some key features implemented in PAIN up to date are calculation of the : * correlation function of the vector * generalized order parameter * frequency dependent generalized order parameter * conformation dependent generalized order parameter * spatial distribution of the internuclear vector orientations * histogram of the dihedral angle (including number of modes and distribution parameters estimation) * conformation transitions analysis Program was tested on and used for an analysis of the MD simulation of the mouse Major Urinary Protein-I in an explicit solvent. |
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