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

Post a Comment

Popular posts from this blog

AutoDock Vina protocol: For Molecular Docking

There are many softwares available for carrying out molecular docking calculations. Many of these softwares are paid, while some of them are free. AutoDock is one such freely available software. Earlier, there was AutoDock 4.0 version available. One of the problem with the software was the space it would occupy, if you attempt to do multi docking. Recently, there is another algorithm made available under autodock. It is called AutoDock Vina. This is more efficient, robust and fast algorithm. There are many tutorials available to learn AutoDock Vina including: http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf and also a video tutorial http://vina.scripps.edu/tutorial.html    But for some reason, few changes or explanation in little detail is always required to make it understandable for a beginner to follow.  Here is a protocol designed in our group, which our Master's student follow to get acquainted to Molecular Docking s
Post a Comment
Read more

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
Post a Comment
Read more

xleap to generate prmtop and inpcrd files

Now that we have the lib file with the information for all the molecules we need to include and also the corresponding combined pdb file, creating prmtop and inpcrd files should not be a difficult task. So, to begin with we have a lib file name: molecule.lib a pdb file for 4 molecules name: four.pdb The  task is to generate a prmtop and inpcrd file. Initiate xleap using: $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99 In xleap window > source leaprc.gaff # load the lib file by: > loadoff molecule.lib I am not sure but some times it helps to also load the frcmod files we created for the four molecules the information of which is stored in the lib file. > loadamberparams aldehyde.frcmod # Load the pdb file: > P=loadpdb four.pdb You should see some thing like this in the xleap window now: ------------------- > P=loadpdb four.pdb Loading PDB file: ./four.pdb Warning: name change in pdb file residue 1 ;  this residue is split i
1 comment
Read more