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Molecular Lab



Overview

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."



File Types

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.

File type/extensionDescription
.pdbThe 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.
.groThe 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.
.topThe molecular topology file combines the forcefield ITP files and with the name of the system and the number of atoms in the molecule.
.mdpThe Molecular Dynamics Parameter file contains all the logistical information required to run a simulation, which includes run time parameters, output controls, and special algorithms.
.trrThe 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.


Inputs

To begin using Molecular Lab, there are three input options that depend on the user's input files.

Input File(s)Description
PDBUser has a molecule yet to be solvated.
GRO, TOPUser has molecule solvated and needs to minimize the energy of the system. Note that GRO and TOP files are products of the solvate process.
TRRUser would like to continue the MD simulation on existing trajectory and simulation parameters.


Flowchart

The flowchart below maps the path Molecular Lab takes in performing MD.



Instructions

Molecular Lab's entire simulation process takes five simple steps.


1. Inputs, PDB and MDP

Choose the input option applicable and upload the pertinent file(s) into Molecular Lab. The input may also be copied and pasted text. As described above, the user may have only a PDB file, TOP and GRO files, or a TRR file.

On the bottom of the window, there is a yes/no question asking whether the user wants to go through the position restrained MD 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

Specify parameters for the energy minimization process. If the user has a TOP file, a window to upload a TOP file is activated. Otherwise, the user is able to choose from a list of force fields.


3. MDP Parameters

If the user specified that they have no MDP file in Phase 1, the user is able to input MDP parameters here. The parameters are divided into different sections such as electrostatics and output control.


4. Preprocessing Run

Preprocessing, which minimizes the energy of the system, is an essential step before the final production run. Here, the user chooses whether to perform a complete production run, which includes preprocessing. If the user chooses no, preprocessing takes place but the simulation ends right before the production run. If preprocessing is successful, a message of success is generated. If the user specified in Phase 1 that they have a TRR file, the user is able to upload their TRR file here.


5. Simulate

To begin the simulation, whether it includes the complete production run or not, click simulate. Preprocessing will take place and if selected, the production run will also take place. When finished, all the output files from various stages of the simulation are displayed for download. Three-dimensional graphics of the initial and final system will also be displayed.



Outputs

After the final production run without restraints is completed, 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.

Molecular Lab generates several different types of output files such as:

  1. Lennard-Jones potential plots
  1. Initial and final configuration images
  1. Trajectory file in a PDB format
  1. 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".



Practice Examples

Example 1: Hepatitis C Virus

  • 2. Upload this PDB file in the first step.
  • 3. In the third step of entering mdp file parameters, enter the following values.
Run and Output Control
Choose an IntegratorMolecular Dynamics
Center of mass optionsLinear
Neighbor Search
Search Algorithmgrid
Periodic boundary conditionsxyz
Electrostatics and Van der Waals
Algorithms to compute Coulomb forcesCut-off
Van der Waals potentialCut-off
Choose a display optionno
Ewald options
Geometry for the Ewald summations3D
Optimize FFTsno
Temeperature/Pressure?
Choose the temperature coupling typeno
GroupsATOMS
Pressure coupling optionsNo pressure coupling
Velocity Generation
Generate velocity?no
Bond parameters
Choose the bond constraint typeno
Choose the constraint algorithmlincs
Choose Yes for an unconstrained startno
Choose Yes to user a Morse potential instead of an harmonic potentialno
  • 4. 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.

Contributors

Contributor NamenanoHUB login or other contact information
Kazutora Hayashidahayaska Stanford University
Artit Wangperawongartitw Stanford University
Eric Darvedarve Stanford University