Computational Biophysics: Files and Configuration



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VMD file is the program that analyses the molecular visualization which plays the DCD trajectory files showing the results of MD simulations. Also, it allows control of running simulations and interactive display when used with the parallel molecular dynamics code namd.
NAMD Configuration files these are the files specifying virtually everything about the simulation to be done. It specifies the dynamic values and options that NAMD uses such as the initial temperature, number of timesteps to perform etc.
The following parameters are required for every NAMD simulation:
•Numsteps: This refers to the number of simulation timesteps to be performed. Only integers greater than 0 are acceptable. Total amount of simulation time = numsteps× timestep.
•Coordinates (PDB file) – This is the PDB file that contains the initial position coordinate data. Path names can be either relative or absolute and only one value may get specified.

•Structure (PSF file) – This is the X-PLOR format PSF file that describes the molecular system to be simulated. It only specifies one value
. Parameters file -These are CHARMM19, CHARMM22, or CHARMM27 parameter file defining all or part of the parameters necessary for the simulation of the molecular system. For each simulation, at least one parameter file must be specified but multiple definitions are only allowed for systems requiring more than one parameter file. The files are read in the order of appearance in the configuration file and if duplicate parameters are read, a warning message gets printed whereby the last parameter value read is used.
Exclude:-This is the parameter that specifies the pairs of bonded atoms to be excluded from non-bonded interactions whereby, the bonded pairs of atoms, with the value of none gets excluded. Also, electrostatic interactions for such pairs gets modified by the constant factor, defined by 1-4 scaling and van der Waals interactions that gets modified using the special 1-4 parameters as defined in the parameter files. The value of scaled1-4 is necessary in enabling the modification of 1-4 VDW parameters present in the CHARMM parameter files.
-Output name- NAMD writes two files at the end of every simulation, one contains final coordinates and another contains the final velocities of all atoms in the simulation. This option specifies the file default prefix for trajectory ad restart files as well as prefix for these two files. Position coordinates are saved to a file named as this prefix with .coorappended while the velocities get saved to a file named as this prefix with .vel appended
• one of the following three: –velocities. – binvelocities. -temperature.
These are the required parameters specifying the most basic properties of simulations would be/tmp/output.coor and /tmp/output.vel.
Q2) The steps that can be used to setup and run the Gramicidin A simulations:
i Build the proteins
ii Replicate lipids
iii Arrange lipids
iv Save positions
v Add water
vi Remove water
vii Fix backbone atoms
viii Restrain CA atoms
In the building part whether we use membrane, in solvent part how big is the water box size? (-t 5 change into some other number). Important parameters used for characterizing simulations need to be changed in NAMD scripts
NAMD Configuration Files are file specifying virtually everything about the simulation to be done. Otherwise, the file specifies what values and dynamics options NAMD should use, such as the initial temperature, the number of timesteps to perform, etc.
-Timestep parameters refers to the number of simulation timesteps to be performed.
-Periodic boundary conditions: NAMD provides periodic boundary conditions in 1, 2 or 3 dimensions. Also, NAMD provides spherical and cylindrical boundary potentials for containing atoms in a given volume.
-Pme: Analyzes all atoms in a system giving the minimum and maximum values of x, y and z coordinates for the entire protein-water system.
-Running time: Run times have been changed to 2 ns and saved every 20 ps.
-Equil.namd:Now build all input files and finally run NAMD. The protocol consists of the following stages: *Minimization with fixed backbone atoms. *Minimization with restrained carbon alpha atoms. *Langevin dynamics with restraints. *Constant pressure with restraints.*Constant pressure without restraints.* Constant pressure with reduced damping coefficients. The NAMD configuration file performs all but the last stage. The following files required by NAMD may be found in the temporary working directory used by VMD for this run.
-Nptsim.namd:The following NAMD configuration file performs the final stage of the simulation.
1- Build the Protein: Build a psf file for the protein. Whereby the original pdb file comes from RCSB protein data bank, access code 1JNO.After finishing building the structure, load both the structure built by psfgen (protein.pdb)and the original pdb file (1JNO.pdb) and compare them.
2 -Membrane
2.1 Build POPE Membrane
To model the flow of water through the Gramicidin channel, use a membrane to separate two water reservoirs on either side of the protein. We will be using the membrane plugin supplied with VMD to generate a solvated and pre-equilibrated POPE membrane.
1. Change to the directory 02_membrane/
2. To build the membrane, run the script called build_membrane.tcl to generate a POPE membrane patch with (approximate) dimensions 40x40x51 Å. The output files are membrane.psf and membrane.pdb. vmd –dispdev text –e build_membrane.tcl
2.2 Align the Protein with POPE Membrane
2.3 Combine the Protein and POPE Membrane
3-Minimize Non-Backbone
It is the first stage of minimizing by fixing the backbone atoms of the protein to minimize everything else.
4- Minimize All
In this stage everything is minimized leaving no fixed atoms and there is need to fix the final output files from min_non backbone.
5 -Restrain CA Atoms
In the VMD script, a trick is used to make sure we are using the last frame in the DCD file for the restraint points.
6- Heat with Restraints
1. Change to the directory 06_heat_restrain/
2. Copy the final output files from minimizing the whole system to the current directory. Use a Unix Terminal window to copy these files:
cp ../04_min_all/min_all.coor . cp ../04_min_all/min_all.vel . cp ../04_min_all/min_all.xsc .
3. Now run the heat_restrain.conf NAMD file: namd2 heat_restrain.conf > heat_restrain.log
7- Equilibrate with Restraints
1. Change to the directory 07_equil_restrain/
2. You need to copy the final output files from minimizing the whole system to the current directory. Use a Unix Terminal window to copy these files:
cp ../06_heat_restrain/heat_restrain.coor . cp ../06_heat_restrain/heat_restrain.vel . cp ../06_heat_restrain/heat_restrain.xsc .
3. Now run the equil_restrain.conf NAMD file: namd2 equil_restrain.conf > equil_restrain.log
Once you have a .xst file, analyze the area of the unit cell with the cell_area script in the scripts directory. Run it with
./cell_area.tcl equil_restrain.xst > equil_restrain.area
Then plot the unit cell area using your favorite graphing program.You can also use namdplot to look at the cell volume, total energy, and other energies you think might be interesting.
8- Free Equilibration

It is usually the last equilibration run and uses the dcd file from the EXAMPLE directory although one may not have time to complete it.
1. Change to the directory 08_equil_free/
2. Copy the final output files from equilibrating with restraints to the current directory. Using a Unix Terminal window for copying these files:
cp ../07_equil_restrain/equil_restrain.coor . cp ../07_equil_restrain/equil_restrain.vel . cp ../07_equil_restrain/equil_restrain.xsc .
3. Now run the equil_free.conf NAMD file: namd2 equil_free.conf > equil_free.log.
Q 3

The Figures above shows the minimization as a platform, in the energy plot, the minimization illustrates that the curve drops quickly and meets a platform. Additionally, heating increases temperature thereby increasing the total energy. The equilibration lets atoms move, after which a platform exists showing the system is stable.

The Figures above illustrate the total energy and temperature,where the blue line for protein without membrane, red line with membrane. There is no more energy that can be dissipated in stretching, therefore energy can only be used to move the molecule through space when the helix is unfolded. However, increase in force per unit time is large to initiate uncoiling of the helix. Similarly, the helix is more rigid and demands at lower temperature.
Screenshot to show the simulation result

Protein with membrane Protein without membrane In general, protein with membrane is stable while the one without membrane will move around and till apart.

The membrane lipid environment is a strong modulator of membrane protein structure and function. A large portion of a membrane protein remains in contact with the membrane lipid environment raising the obvious possibility of the membrane being an important modulator of membrane protein structure and function. This is seen when increasing membrane protection of the proteins during heating. The simulation of gramicidin rotameric states in vacuum, shows that stacking conformations are strongly disfavoured. This suggests a specific role for the lipid environment in the possible stabilization of such a conformation.

Comparison of structural changes with or without membrane

Without membrane

When we use with or without membrane, we notice that the RMSD with membrane changes a little during the simulation.
Tryptophan residues of gramicidin play an important role in channel conductance and gramicidin structure because it is an integral component of channel activity and a thermodynamically preferred conformation of gramicidin in membrane environments.
Gramicidin is a very hydrophobic peptide and the four C-terminal tryptophan residues In lipid bilayer membranes, gramicidin dimerizes & folds as a right-handed ?-helix. The helix itself is not long enough to span the membrane, but it dimerizes to form the elongated channel needed to span the whole membrane and the dimer just spans the bilayer.
And due to the dihedral angle combinations generated in the conformation space, gramicidin represents a useful model for realistic determination of conformational preference of proteins in a membrane environment
The membrane structure are very hydrophobic and suffer from poor water solubility and lack of bacteria-specificity. Thus gramicidin A charged residues readily become neutral upon membrane binding and the building blocks affording water-solubility of the peptide without sacrificing its membrane permeability
Lipids are non-polar (hydrophobic) compounds which are soluble in organic solvents. Most membrane lipids are amphipathic, having a non-polar end and a polar end. Also, they have small portions that are hydrophilic and large hydrophobic portions (non-polar). Examples of lipids include fats, oils, waxes, phospholipids, sterols, certain vitamins, hormones and most of the non-protein membrane of cells. Lipid bilayers formed provide barrier to the flow of polar molecules separating the hydrophilic head of the lipid molecule on the outside surface of cell membrane and the hydrophobic fatty acid long chains on the inside of the lipid bilayer.
i. Water models are techniques developed to discover the water structure. The water molecule shows positive and negative polarity with oxygen “side” being negative charged and hydrogen “sides” is positive. The oxygen side binds to positively charged ion or molecule, and hydrogen side to negatively charged ion or molecule.
Membrane lipids molecules have both hydrophilic and hydrophobic moieties forming closed bimolecular sheets. The lipid bilayers formed provide barrier to polar molecules flow. The hydrophilic head of the lipid molecule is on both the outside and inside surface of the cell membrane while the hydrophobic fatty on the outside.


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