5/9/2021 0 Comments Pymol Viewer For Windows 10
You also agree to the Terms of Use and acknowledge the data collection and usage practices outlined in our Privacy Policy.It models protein or other molecules as a harmonic oscillating system and classifies all possible deformations around a stable equilibrium.Abstract In order to get the dynamic molecule model from the static one, the molecular dynamics (MD) simulation needs to be performed.
Pymol Viewer Software Sets SuchSome software sets such as GROMACS are used for that purpose.The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from the PyMOL software by GUI-based interface of GROMACS tools. This paper describes many improvements introduced into the Dynamics PyMOL plugin 2.0 including: an integration with ProDy library, possibility to use the implicit solvents, an ability to interpret the MD simulations, and implementation of some more GROMACS functionality. Keywords: Dynamics, GROMACS, Plugin, PyMOL Introduction Structures of molecules obtained from X-ray crystallography 1, nuclear magnetic resonance 2, and other methods 3 are stored in the Protein Data Bank 4, 5. They are formatted as PDB files 6 and one of the most popular software to visualize them is PyMOL 7. One of the software that allows molecular dynamics (MD) simulations is GROMACS 8 12. PyMOL exposes an API for third party plugins 13, we took advantage of that fact and the Dynamics PyMOL plugin 14 was developed to facilitate molecular dynamics simulations in PyMOL GUI, using the underlying GROMACS. Performing molecular dynamics simulation is a relatively complicated task, therefore every option to reduce level of complexity of calculations is welcome. One of such options is the reduction of the number of interacting centers through the use of an implicit solvent model. Although the explicit solvent is still the standard solution model in molecular dynamics simulations and GROMACS offers TIP3P, TIP4P, SPC, and their variants as a water model 15, the calculation using thousands of those water molecules is computationally demanding, as they interact not only with the molecule of interest, but with each other as well. The system with explicit solvent needs to be placed into the so-called water box. The water box, if used without the proper periodic boundary conditions, would lead to undesired border effects, which could disturb the whole simulation. Those limitations were stimulus to develop other methods of handling solvent in molecular dynamics simulations. GROMACS offers implicit solvent as an alternative and exposes three generalized Born (GB) implementations: Still, Hawkins-Cramer-Truhlar (HCT), Onufriev-Bashford-Case (OBC) 16. The results of the molecular dynamics simulation can be visualized as an animation. Those animations give researchers important information about movement of the molecule, but usually they are not enough. In order to obtain more data from the system it is critical to perform proper analysis of the MD results. The correct interpretation of MD data can produce static images presenting the results of dynamic behavior of the molecule shown in the form of, for example, vectors pointing into direction of the highest displacement of the molecular fragment. It also provides quantitative interpretation of the results, which can be used for comparison with other simulations or for further analysis. Two methods are particularly useful in aiding the interpretation of MD results, these are the normal mode analysis (NMA) and the principal component analysis (PCA).
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