It involves the interaction between all pairs of atoms excluding the bonded atom as it is already involved in bonded term. For weak dipole attraction and repulsion depending upon distance between atoms is accounted by the Leonard-Jones potential which Is given by:- 2) VIM :- It is a program for molecular visualization, modeling and analysis of biological systems like proteins, nucleic acid, and lipid belayed assemblies. VIM also gives option to work with volumetric data, sequence data, and arbitrary graphics objects. VIM includes TIC and Python interpreters, so users can run their own script f these.
VIM is preferred over others program because of its following unique features :- can operate on multi-globally molecular dynamic trajectories. Interoperability with a large number of simulation packages. Its ability to integrate structure and sequence information. Other key features are:- Visualization of 3-D molecular with deferent patterns. Can display and select subsets of atom from atom selection syntax. Can visualize dynamic molecular and volumetric data. Major molecular data file formats are supported. Capability of movie making. Interactive molecular dynamics simulation.
Adjustment of structure to the force field. Relaxing the strained contacts created by guessing coordinates of atoms during generation of SSP file. Finding local minimum energy conformation for potential energy function. Minimization does not give the global minima. It is done for achieving the energetically stable conformations. Minimization is carried out for 35000 steps at temperature using NAMED. 5) After minimization, water box is added using VIM. This water coordinates is obtained from pure water simulation to mimic the solvent condition inside the cell.
One of the most important effect of solvent is screening o electrostatic interaction. 6) once again, minimization is done for the same reasons. 7) Now, ions are added to solvate protein to neutralize the excess charges, so that force field and energy parameters don’t get influence by charges. 8) Again, SSP is generated using VIM. 9) Minimization is again done at this step. 10) Heating of Gauge using NAMED after minimization :- It is done Because of:- Under this, the protein system is heated to a desired temperature with a linear increase from K to kick with a increase ion. 1 K at each step. So the total step of Maxwell distribution. 1 1) Minimization is once again done after heating. 12) Equilibration of Gauge system using NAMED for:- Ensuring that system is in stable state after heating. Making the properties like pressure, temperature, and energy sat equilibration. Equilibrating and distributing the kinetic and potential Energies equal among all degrees of freedom. With time of Equilibration is nothing but simulating a unstable protein system for making it stable. It is done at kick. 13) simulation of Gauge system is done using NAMED at kick.