Adventures in Computational Chemistry

Vibrational frequency calculation holds a key that can decide whether the obtained optimized structure is a minimum or a transition state or some thing else. I always wanted a simplistic adaptation with minimal understandable and required information that in a matter of minutes can help a new person understand the concept as easily as possible. Finally I found this link: http://openmopac.net/manual/Hessian_Matrix.html which makes it really easy for anybody. So, what we least need to know when you submit a frequency calculation. In frequency calculation also called force calculation, we are solving a hessian matrix. What is a Hessian matrix? The Hessian matrix is the matrix of second derivative s of the energy with respect to geometry. What is the trouble in frequency calculation? Although first derivatives are relatively easy to calculate, second derivatives are not. To overcome this problem, the double derivative is evaluated in terms of first der

An extension of earlier problem in generation of prmtop and inpcrd files follows here. After a long time I had to use xleap to generate parameter and coordinate files for a system comprising of an organic molecule, protonated methanol and Cl atom. Now, organic molecule is not an issue. antechamber tutorial clearly explains how to do that. So, any organic molecule like MEOH is also not a problem. But MEOH2 could be. I have written about how to deal with systems like MEOH2 or extra protonated oxygen systems. But if you want to bring an organic molecule, protonated methanol(MEOH2) and Cl atom together and create parameter and coordinate file for that, it may not be as easy as it appear. Since I had lost touch with xleap for sometime, I totally forgot the small tricks I found to work in xleap. I started working with: * the separate pdb files for each molecular unit. * then create a single pdb file using packmol for the whole system. * create prepin or mol2 file corresponding to combined p

 In the previous post I mentioned about using mol2 file for parameter file generation for protonated systems like this. I mentioned how it is easier to work with mol2 files in this case over prepin files. I ended up creating a mol2 file which appeared sensible consider the definitions of different atoms in the molecule. I missed one thing then, which I rectified to get calculations going ahead. After I created the parameter files and started working with them, I realised there is a small issue with the molecule. I found out that the extra proton on oxygen  although is located close to the desired oxygen, it does not show any bond between the proton and the oxygen. Initially I was went impression that this could be an issue with xleap in visualization. But this actually is a problem. If not immediately you will realise it sooner when calculations start giving odd results or crash instantaneously. Three things need to be carefully checked: First the extra proton some times is

I am working on a system that closely resembles this : The oxygen is protonated so that there are three bonds involving oxygen. I tried to create the prmtop and inpcrd files for this system using antechamber and xleap. Using Antechamber, if I try to create to parameter files by using prepin file, I encounter lot of problems. Initially I used a pdb file of the molecule generated using either vmd or molden. But antechamber finds error in running bondtype. So, I shifted to gabedit to generate the structure and creating its pdb file. This works fine. Atleast antechamber does not get bondtype error here. But, then, if you try to create prepin file using command: $AMBERHOME/exe/antechamber -i F.pdb -fi pdb -o F.prepin -fo prepi -c bcc -s 2 you will face errors related to the charge on the system like: INFO: Number of electrons is odd: 127       Please check the total charge (-nc flag) and spin multiplicity (-m flag) As suggested you need to use -nc and -m flags to take

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 dif

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 probabilit

The two words in the title literally means: Molecular : of or relating to molecules Dynamics : the pattern or history of growth, change, and development in any field Thus Molecular Dynamics tells you about a pattern or history of growth, change and development of molecules in any environment. It is a computational method which allows one to understand time dependent movement of atoms and molecules. These movements of molecules are predicted based on the Newton's law of motion. The resulting forces on these atoms and molecules and their potential energy are defined with the help of different molecular mechanics force fields. The Force fields consists of defined parameters like bond length, bond angles, torsions, Vander Waal forces etc. These force fields are specific for the kind of molecules treated. Thus, the force fields vary in nature depending on the parameters included and the type of target molecules. So, it is always advisabl

Returning to xleap again. The box I require this time has little tricky requirements. 1) The box should satisfy the molarity ratio for the solute: solvent. 2) Should be big enough that QMMM calculations can be carried out easily 3) combine sets of molecule-pairs which are interconvertible following a proton transfer. I have a pair of molecules say p(H)--i which can be converted to another set called P--I(H) following a proton transfer from p to i.So, p(H)--i <---> P-I(H) To fulfill condition (1), I initially created one molar box for p(H)--i called "PIN" and other box for P--I(H) called "PII" For condition (2) and (3), I created a bigger box with 7 PIN and 1 PII boxes. The idea is: after proton transfer from I to P, during the QMMM calculation, P--I(H) pair coming from "PII" should convert to p(H)--i pair like other pairs from "PIN" and the whole box should become homogeneous with 8 p(H)--i pairs. We begin with: PIN with