Current status of protein force fields for molecular dynamics simulations
Pedro E M Lopes1, Olgun Guvench, Alexander D MacKerell
1Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street HSFII, Baltimore, MD, 21201, USA.
Methods in Molecular Biology (Clifton, N.J.)
|October 22, 2014
Summary
This review covers classical protein force fields, comparing additive CHARMM36 with Drude and AMOEBA polarizable models. Molecular simulations highlight the performance of these advanced force fields for proteins and peptides.
Area of Science:
- Computational Chemistry
- Molecular Dynamics
- Biophysics
Background:
- Classical force fields are essential for simulating protein behavior.
- Additive force fields have been widely used, but polarizable models offer improved accuracy.
- The development of advanced force fields is crucial for understanding protein dynamics.
Purpose of the Study:
- To review the current state of classical protein force fields.
- To compare additive force fields with emerging polarizable models like Drude and AMOEBA.
- To summarize simulation results demonstrating the performance of these force fields.
Main Methods:
- Review of existing literature on protein force fields.
- Description of parametrization strategies for the Drude force field.
- Comparison of Drude and AMOEBA force fields with the CHARMM36 additive force field.
- Analysis of molecular simulation results for proteins and peptides.
Main Results:
- Additive force fields like CHARMM36 provide a baseline for protein simulations.
- Drude and AMOEBA polarizable force fields show promising results in molecular simulations.
- Specific parametrization strategies enhance the performance of the Drude force field.
- Simulations illustrate the capabilities of polarizable force fields for studying proteins and peptides.
Conclusions:
- Polarizable force fields represent a significant advancement in protein simulation accuracy.
- Continued development and validation of Drude and AMOEBA force fields are warranted.
- These advanced force fields will enable more precise investigations into protein structure and function.
Related Concept Videos
01:13Force and Potential Energy in One Dimension
4.8K
Force can be calculated from the expression for potential energy, which is a function of position. The component of a conservative force, in a particular direction, equals the negative of the derivative of the corresponding potential energy with respect to the displacement in that direction. For regions where potential energy changes rapidly with displacement, the work done and force is maximum. Also, when force is applied along the positive coordinate axis, the potential energy decreases with...
4.8K
01:58Mechanical Protein Functions
4.4K
Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.
4.4K
01:30Three-Dimensional Force System
3.2K
In mechanical engineering, a three-dimensional force system is a system of forces acting in three dimensions, with forces applied along the x, y, and z coordinate axes. The three-dimensional force system is an important concept in mechanical engineering, as it allows engineers to understand and analyze the behavior of objects and structures in three dimensions. By understanding the forces acting on a system, engineers can design more efficient and effective mechanical systems that can withstand...
3.2K
01:09Types of Forces
11.9K
In most situations, forces can be grouped into two categories: contact forces and field forces. Contact forces occur as a result of direct physical contact between objects. Field forces, however, act without the necessity of physical contact between objects. They depend on the presence of a "field" in the region of space surrounding the body under consideration. You can think of a field as a property of space that is detectable by the forces it exerts. Scientists think there...
11.9K
01:04Force and Potential Energy in Three Dimensions
3.8K
Consider a particle moving under the action of a conservative force that has components along each coordinate axis. Each component of force is a function of the coordinates. The potential energy function U is also a function of all three spatial coordinates. Force in one dimension can be written as the negative ratio of potential energy change to the displacement along that coordinate. For minimal displacement, the ratios become derivatives. If a function has many variables, the derivative only...
3.8K
01:06Force
25.9K
Forces affect every moment of our life. Our bodies are held to the Earth by force, and they are held together by the forces of charged particles. When we open a door, walk down a street, lift a fork, or touch a baby's face, we are applying force. Our body's atoms are held together by electrical forces, and the core of an atom, called the nucleus, is held together by the strongest force known to us—nuclear force.
The study of motion is called kinematics, but kinematics only...
The study of motion is called kinematics, but kinematics only...
25.9K