Skip to main content

Statistical Ensemble

An Ensemble provides the physical description of the system.

A system can be completely described interms of the three components of the velocity and position each for every atom in the system. But, this is an almost impossible information to collect.

Instead, while describing a system, people use measurable average properties like energy, pressure etc. These properties do not depend on the individual characterization of each constituting atom of the system.
But, at the same time these properties also do not characterize the system completely.

One set of values of these properties may correspond to different states of the system. Based only on one set of properties thus, it is thus difficult to pinpoint at a particular state of the system. So every possible state of a system has equal probability corresponding to a value of measurable average property .

At a given time, the system can be in only one state. If the same system with one set of properties is considered exisiting at different time steps are considered, it is found to exist in different states.Each such different state of a system which can be characterized by the same set of measurable average properties are called ensemble. Statistical mechanics deals with ensemble instead of individual systems.

Depending on the properties used to define a system there are different ensembles:

Microcanonical ensemble (NVE) : The ensemble characterized by a fixed number of atoms, N, a fixed volume, V, and a fixed energy, E. Thus it is isolated from changes in moles (N), volume (V) and energy
(E). Since the total energy for the system remains constant, no energy is lost in the form heat exchange, that makes the the system adiabatic in nature.


Canonical Ensemble (NVT): The ensemble is characterized by a fixed number of atoms, N, a fixed volume, V, and a fixed temperature, T. Since the temperature in this ensemble remains constant, the energy needs to be exchanged with the surrounding which can be done with the medium of thermostat.

Isobaric-Isothermal Ensemble (NPT): This ensemble is characterized by a fixed number of atoms, N, a fixed pressure, P, and a fixed temperature, T. In addition to a
thermostat, a barostat is needed.

Grand canonical Ensemble (mVT): The thermodynamic state for this ensemble is characterized by a fixed chemical potential, m, a fixed volume, V, and a fixed temperature, T.

Comments

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

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

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