|Version 34 (modified by artitw, 7 years ago) (diff)|
Molecular Lab is a tool that models large biomolecules through the computer simulation technique known as Molecular Dynamics (MD). Made possible through the Network for Computational Nanotechnology, Molecular Lab is available on http://www.nanohub.org. The purpose of this wiki is to familiarize the user with Molecular Lab.
Molecular Lab integrates the MD computational power provided by GROMACS into a user-friendly GUI. By following each of the tabs of the GUI, the user can upload files and input various parameters conveniently without ever having to deal with the complex process of MD simulation through GROMACS. From the GROMACS website http://www.gromacs.org: "GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers."
Below are brief descriptions of the files essential to running Molecular Lab. For more detailed information, see the GROMACS reference manual http://www.gromacs.org/external/online-reference-manual.html.
|.pdb||The Protein Data Bank file contains the atoms of the molecule of interest and their xyz positions. The PDB file is the first input for the first stage of Molecular Lab. For more information about PDB files, visit http://www.rcsb.org/pdb/home/home.do. This Web page also contains PDB files of various protein molecules which may be viewed and downloaded.|
|.gro||The Gromos file is a molecular structure file very similar to the PDB file. This file is usually created after the molecule of interest has been solvated. The GRO file may also include the xyz velocities of each atom for initial conditions.|
|.top||The molecular topology file combines the forcefield ITP files and with the name of the system and the number of atoms in the molecule.|
|.mdp||The Molecular Dynamics Parameter file contains all the logistical information required to run a simulation, which includes run time parameters, output controls, and special algorithms.|
|.trr||The Binary Trajectory file contains the trajectory of the simulation, which includes all coordinates, velocities, forces, energies, and user-specified MDP information. It can also be used as input to continue a simulation. Pymol (http://pymol.sourceforge.net/) may be used to view TRR files.|
To begin using Molecular Lab, there are three input options that depend on the user's input files.
|PDB||User has a molecule yet to be solvated.|
|GRO, TOP||User has molecule solvated and needs to minimize the energy of the system. Note that GRO and TOP files are products of the solvate process.|
|TRR||User would like to continue the MD simulation on existing trajectory and simulation parameters.|
The flowchart below maps the path Molecular Lab takes in performing MD.
Molecular Lab's entire simulation process takes five simple steps.
|1. 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. When the user tries to upload a file onto Molecular Lab, a pop-up window like the following appears.
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.
2. 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.
3. 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.
4. 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. This is an essential step before the final production run that minimizes the energy of the system.
6. Simulate 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.
3.1 Program Outputs Description
After the final mdrun without restraints is done, Molecular Lab allows the user to download several different files. The tool allows the user to download the output GRO, TOP, MDP and TRR files. In addition to the file downloads, the tool also visualizes the input and output molecule in a small screen. To get a more detailed dynamic visual output, the user has to download the TRR file and input the file into a visualization tool such as Pymol. Below is Hepatitis C Virus visualized by Real VMD. As explained earlier, TRR file includes information about the dynamics of the molecule inside water, so the by using visualization programs, the user is able to see how molecules interact with water from various different angles. Other files such as GRO and TOP can be downloaded so that they can be reused when the user wants to repeat the same reaction but with different MDP parameters. This way, the user does not have to start from scratch and can save some time by skipping the solvate step.
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".
4.1 Practice Examples
Example 1 Hepatitis C Virus
- Download the PDB file of hepatitis C virus from http://www.rcsb.org/pdb/explore.do?structureId=1R7E.
- Upload this PDB file in the first step.
- In the third step of entering mdp file parameters, enter the following values.
|Run and Output Control|
|Choose an Integrator||Molecular Dynamics|
|Center of mass options||Linear|
|Periodic boundary conditions||xyz|
|Electrostatics and Van der Waals|
|Algorithms to compute Coulomb forces||Cut-off|
|Van der Waals potential||Cut-off|
|Choose a display option||no|
|Geometry for the Ewald summations||3D|
|Choose the temperature coupling type||no|
|Pressure coupling options||No pressure coupling|
|Choose the bond constraint type||no|
|Choose the constraint algorithm||lincs|
|Choose Yes for an unconstrained start||no|
|Choose Yes to user a Morse potential instead of an harmonic potential||no|
- Download the output .trr file and input it into a graphics program like VMD or Pymol. The following is an post-simulation image created by VMD.
|Contributor Name||nanoHUB login or other contact information|
|Kazutora Hayashida||hayaska Stanford University|
|Artit Wangperawong||artitw Stanford University|
|Eric Darve||darve Stanford University|