|Version 3 (modified by hayaska, 7 years ago) (diff)|
Introduction to Hydrolab
1.1 Overview of Molecular Lab
Molecular Lab is a free molecular dynamics simulation tool that part of the nanoHUB project, which is spearheaded by Network for Computational Nanotechnology (NCN). The tool is available on the nanoHUB website, www.nanohub.org
Molecular Lab allows the user to input any molecule written in the PDB (Protein Data Bank) format. PDB format is a file format specified by Protein Data Bank (http://www.rcsb.org/pdb/home/home.do). PDB format specifies the types of atoms and their positions in x, y and z co-ordinates. PDB files of various molecules can be viewed and downloaded from the PDB website. In this software, you will be able to tune the interaction between water and molecules of any type.
Calculations of the actual molecular dynamics simulation are performed by simulation software called GROMACS. Capabilities of the software can be seen on the GROMACS website, www.GROmacs.org. GROMACS takes various input files in different formats, but Molecular Lab simplifies the entire simulation process into a friendly Graphical User Interface (GUI). By following each step in the top tabs of the GUI, the user can upload files and input various parameters without ever having to deal with the complex process of MD simulation of GROMACS.
2.1 Program Inputs
Molecular Lab follows the basic Molecular Dynamics simulation process of GROMACS, a MD simulation program. There are some main file types involved in a standard GROMACS simulation process. There are detailed explanations of these file types on the GROMACS website. (http://www.gromacs.org/external/online-reference-manual.html).
Here is a list and brief explanations of important file types involved in Molecular Lab
PDB file: Protein Data Bank (PDB) file is the first input file format for the first stage of the MD simulation process. PDB file contains information about the types of atoms and their positions in the input molecule. Output files are created based on the content of the PDB file.
GRO file: GRO file format is a structure file format very similar to the PDB file format. This is the format of the file that is created after the molecule written in the PDB format is mixed with water. GRO file can also include the velocities of each atom in x, y and z directions.
TOP file: TOP is a topology file format that includes information about the number of solvent and water molecules and bond parameters. TOP file is created after the molecule is mixed with water.
MDP file: MDP is a dynamic file format that includes information about all essential bonding parameters and other information pertinent to mdrun simulation step. The user is able to specify maximum bond angles and other information that determines the accuracy of the simulation.
TRR file: TRR is a trajectory file format that includes information about the final mdrun simulation step recorded every pre-specified time step. TRR file can be downloaded and input into visualization tools like Pymol to view the simulation process.
The following flowchart represents the overall MD simulation process with Molecular Lab. Although the actual simulation steps involved in the GROMACS simulation include many steps, Molecular Lab has simplified the entire simulation process into 5 simple steps. There are only 3 different patterns where the user inputs files to Molecular Lab. As described in the flowchart, in Pattern 1, the user has the input PDB file where the molecule is yet to be mixed with water. In Pattern 2, the user already has GRO and TOP files and uploads them onto Molecular Lab. In this situation, the simulation starts from the energy minimization process instead of solvate process, since GRO and TOP files are products of the solvate process. In Pattern 3, the user already has the final TRR file before the final mdrun. In this case, Molecular Lab only goes through the final mdrun without restraints. As mentioned earlier, Molecular Lab consists of 5 phases. Here is a list of explanations for each step.
- PDB and MDP
The user is asked to choose the situation that applies to them from having only PDB file, having TOP and GRO files, and having TPR file for the final mdrun. Depending on the choice, certain inputs are blocked in other phases, so that the user can easily recognize what files need to be uploaded. In addition, the user is able to upload their PDB or gro file on this phase. On the bottom of the window, there is a yes/no question asking whether the user wants to go through the position restrained mdrun process. For MDP files, the user has the option of either uploading the file or filling a form, from which an MDP is automatically created.
- Box generation and energy minimization
In this phase, the user is asked to specify various parameters for the energy minimization process. Depending on whether the user has a TOP file or not, a window to upload a TOP file is activated or not. Otherwise, the user is able to choose from a list of force fields.
- MDP file parameters
If the user answered that they have no MDP file in the phase 1, the user is able to input MDP parameters in this phase. The parameters are divided into different sections such as electrostatics and output control. The user’s inputs are directly substituted into an MDP file, which is used in the position restrained and final production run.
- Preprocessing run
The user chooses whether they wish to have the final production run. If the user chooses no, the simulation stops right before the production run and when successful returns a message of success. If the user chose in phase 1 that they have a TPR file for the final mdrun, the user is able to upload their TPR file at this point.
As soon as the user clicks the simulate button, the simulation automatically starts. This includes all the pre-processing steps or, if selected, the production run. When successful, all the output files from various stages of the simulation are displayed for download. The user is also able to view the 3D graphics of the starting and final molecular configurations.
Lennard Jones potential, expresses the strength of repulsion and attraction of two particles with varying distances. Below is a sample Lennard Jones potential plot.
- Short range repulsion can be observed in the region where the potential is more than 0 and the intermolecular separation is less than the equilibrium distance.
- Long range weak attraction can be observed in the region where the potential is less than 0 and the intermolecular separation is more than the equilibrium distance.
- Equilibrium position can be observed at the well of the curve, where the potential reaches its minimum.
3.1 Program Inputs Description
- C6 corresponds to and C12
corresponds to of the Lennard-Jones potential, . The default values are shown below.
- The temperature parameter allows the user to input any value
between 0 and 1000 Kelvin. The default temperature is 300 Kelvin.
- The initial configuration parameter has two options. The high
concentration creates a simulation box with a higher concentration of hydrocarbons and the low concentration creates a simulation box with a lower concentration of hydrocarbons. Note that the simulation box size stays constant at 3nm x 3nm x 3nm.
- The time step parameter specifies the number of time steps the
simulation takes. Each time step is 0.001 pico seconds. The number of time steps can vary between 2 and 500000 steps. The default value is 1000 steps.
More time steps increase the simulation time.
- The PDB content has the options of generating the trajectory files
of carbon atoms only, water molecules only or both. We recommend that you save the trajectory file with a “.pdb” extension onto your local machine. You can then view the trajectory using this file with your preferred molecular visualization tool. We recommend VMD or Pymol.
Link to PDB format:
Link to VMD:
Link to Pymol:
4.1 Program Outputs Description
Hydrolab generates several different types of output files such as:
- Lennard-Jones potential plots
- Initial and final configuration images
- Trajectory file in a PDB format
- Log file of the simulation run
These files can be saved either by using the download button next to the scroll down icon or scroll down and click "download".
5.1 Shapes of the Lennard-Jones plots
Follow the steps below to observe the effects of epsilon and sigma values on the shape of the Lennard-Jones plots.
- For C-C interaction, assume sigma=0.337nm and
epsilon=1624kJ. Compute C6 and C12 and observe the minimum point and the x-intercept of the Lennard Jones potential curve.
- Multiply epsilon by 2, compute C6 and C12 again and observe the
- Multiply sigma by 2, compute C 6 and C12 and observe the
- Comment on your observations.
6 Clustering and Dissolution of Hydrocarbons in Water
Now, observe the effects of the strengths of C-C and C-O bonds on the clustering of the hydrocarbons. After mixed with water molecules, hydrocarbons can act in three different ways: clustering into a sphere, clustering into a slab, and dissolution into water.
The number of time steps must be set to 10000 for all the procedures below.
6.1 Spherical Clustering
Spherical clustering occurs when there is a low concentration of hydrocarbons and strong C-C bonds and weak C-O bonds. Observe the spherical clustering of hydrocarbons for low concentration of hydrocarbons.
- Run a simulation with the default bond strengths and observe the
shape of the hydrocarbon clustering. It should be close to a sphere.
- Multiply C6 C-C by 10, run the simulation again and observe the
clustering of the hydrocarbons into a perfect sphere.
- Additional simulation: set the bond strengths back to the default
and divide C6 C-O by 100, run the simulation and observe the clustering of the hydrocarbons into a sphere.
Spherical clustering visualized by VMD
6.2 Slab Clustering
Slab clustering occurs when there is a high concentration of hydrocarbons inside the box. This is due to the periodic boundary conditions imposed on the system.
Hence, repeat the above steps by changing the concentration to high concentration. In each case, you should observe hydrocarbon clustering into a slab.
Slab clustering visualized by VMD
6.3 Dissolution in Water
Dissolution of hydrocarbons into water occurs when C-C bonds are weakened and C-O bonds are strengthened. This situation is similar to polar molecules or ionic molecules in water. Follow the procedures below to observe hydrocarbons dissolving in water.
- Multiply C6 C-O by 400, run the simulation and observe the final
arrangements of hydrocarbons.
- To observe the scattering of hydrocarbons better, download the
trajectory file in a PDB format and save it as a “.pdb” file. Use your preferred molecular visualization program on your local computer to view the scattering of the hydrocarbons.
Dissolution of hydrocarbons in water visualized by VMD
|Contributor Name||nanoHUB login or other contact information|
|Eric Darve||darve Stanford University|
|Kazutora Hayashida||hayaska Stanford University|