NOVÁK, Petr, Lukáš ŽÍDEK, Pavel MACEK, Petr PADRTA and Vladimír SKLENÁŘ. Program for Analysis of Internal Motion in Molecular Dynamics Simulation. In Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul". Brno: Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta, 2007, 1 pp.
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Basic information
Original name Program for Analysis of Internal Motion in Molecular Dynamics Simulation
Name in Czech Program pro analýzu vnitřních pohybů v molekulové dynamice
Authors NOVÁK, Petr, Lukáš ŽÍDEK, Pavel MACEK, Petr PADRTA and Vladimír SKLENÁŘ.
Edition Brno, Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul" 1 pp. 2007.
Publisher Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta
Other information
Original language English
Type of outcome Proceedings paper
Field of Study 10403 Physical chemistry
Country of publisher Czech Republic
Confidentiality degree is not subject to a state or trade secret
Organization unit Faculty of Science
Keywords in English MD; PAIN; protein; dynamics;
Tags International impact
Changed by Changed by: prof. Mgr. Lukáš Žídek, Ph.D., učo 38990. Changed: 9/4/2010 13:44.
Abstract
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.
Abstract (in Czech)
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.
Links
GD204/03/H016, research and development projectName: Strukturní biofyzika makromolekul
Investor: Czech Science Foundation, Structural biophysics of macromolecules
MSM0021622413, plan (intention)Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment
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