Skip to main content

Statistical mechanics/Thermodynamics



The previous post hints about the contribution of Statistical mechanics in Molecular Dynamics.
Looking at the definition of the words Statistics and Mechanics:

Statistics is the science that deals with the collection, classification, analysis, and interpretation of numerical facts or data, and that, by use of mathematical theories of probability, imposes order and regularity on aggregates of more or less disparate elements.

Mechanics is the branch of physics that deals with the action of forces on bodies and with motion, comprised of kinetics and statics.

If in addition if one learn the definition of thermodynamics, a science concerned with relation of heat, work and energy and their interconversions, one can try to understand statistical mechanics/ thermodynamics and its connection with Molecular dynamics.

Thus in Statistical mechanics/ thermodynamics one applies the mathematical theories of probability to study thermodynamic behavior associating heat, work and energy of systems composed of large number of particles which are mostly in motion owing to action of forces on these particles.

Thus Statistical mechanics/Thermodynamics acts as a bridge in the form of probability theory connecting microscopic properties of individual atoms and molecules to the thermodynamic properties of the system formed from these microscopic particles.

Statistical thermodynamics calculates the distribution of a given amount of energy E over N identical systems. It helps to interpret the measurable macroscopic properties of system as a function of properties of the constituent particles and the interactions between them. This is done by connecting thermodynamic functions to quantum-mechanical equations. Partition function and the Boltzmann distributution function are the two important pillars of the bridge of statistical thermodynamics connecting bulk thermodynamic properties and the individual atom/molecular properties.


Another factor important from the point of view of Statistical thermodynamics is the physical description of the system. An ensemble provides this physical description which crudely is a collection of all possible configurations of the system with different microscopic states but an identical macroscopic or thermodynamic state.

 For a simplified graphical tour of Statistical thermodynamics, no better place than this link:
http://www.physics.sfsu.edu/~gmarcy/smgraphical.html

Comments

Popular posts from this blog

Material Studio - selective molecule movement

So, working with Material Studio is awesome. You get to handle bigger, complicated and even unimaginable system. But I am facing problems in very minute functioning. I recently faced two problems, but managed to resolve on my own. Somehow, tutorials doesn't help in resolving them and you end up doing some exercise on your own to get the solution. Among these, the problem of bringing two molecular structures in one window and then adjusting one molecule by moving it around, while other structure remains untouched, as it is. Actually, this should not be a problem to do. There is a simple way of doing this. Select the molecule to be moved and then there is a symbol (button) to select, which allows you to selectively move that molecule only. This is the same way it can be done in Material studio too.  But among all the dozens of symbols, the new person handling MS, kind of gets lost. So, what he does is check the tutorials, for any help. But the tutorials don't talk about suc...

Conditions to use different Schrodinger Equation forms

Every molecular system has an energy associated with it. This energy might show a shift depending on the surrounding environment or internal variations. Magnetic dipoles present in a molecular system in the form of electrons and the nuclei is one such reason for the energy shift. But the effect of these magnetic dipoles on the energy shifts will be much less which can be accounted by considering perturbation theory. Chemical binding energies on the other hand are responsible for the major shifts in energy of a molecular system. Thus the focus is shifted towards the valence electrons responsible for most of the chemical activity of a molecule. The valence electrons are separated from the core electrons. The core electrons are treated approximately. This reduces the efforts of considering the relativistic effects affecting the core electrons, and thus can now be ignored. What are relativistic effect? It has been nicely explained by Ermler and Pitzer in the introduction of th...

Generating a structure PDB file using Gabedit

If Gabedit is installed and functioning on your system, type gabedit  in terminal. Gabedit will open and you can find an option "Geometry" in the tool bar. Select "Geometry"--> "Draw" After some trials and playing you will finally learn how to generate a structure. Once your structure is ready, you need to set the atom types and charges. For this click on "M" button in the top left of the "Draw Geometry" window and select options as: M-->"Set"--> "Atom Type & charge using PDB template" Here if you use "Atom Types using connection types", it helps. You can check if the atom type and charge has been set according to the amber requirements by an indirect method. Try to run a quick MM calculation. Run MM calculations by clicking: "M"-->Molecular Mechanics-->optimization It may sometimes end up with a pop up window that suggests that either atom type or charge is not...