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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. For more information, see GROMACS's website http://www.gromacs.org.



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.
.itpThe Include Toplogy file contains the forcefields for the atoms. This file is to be included in topology files (.top extension).
.topThe Molecular Topology file combines the forcefield ITP files 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. Note that this is a binary file and support for binary file uploads to Molecular Lab is still in development.


Flowchart

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



Instructions

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


Uploading files

Whenever the user chooses the upload option, a new window will pop-up as shown below and the user may browse the local machine for the desired file. After clicking Upload, the window will return to the main Molecular Lab window. Please disable any pop-up blockers for www.nanohub.org.


1. PDB and MDP

Choose the input options 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. Note that support for binary file uploads to Molecular Lab is still in development.

Notice in the bottom of the screen image below that the user has the option of either uploading the MDP file or filling in values in Step 3 to manually create an MDP file through Molecular Lab.


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 uploads no MDP file in Step 1, then the user inputs MDP parameters here. The parameters are divided into eight different sections:

(1/8)Run and Output Control
(2/8)Langevin Dynamics
(3/8)Neighbor Search
(4/8)Electrostatics and Van der Waals
(5/8)Ewald options
(6/8)Temperature/Pressure?
(7/8)Velocity generation
(8/8)Bond Parameters


4. Preprocessing Run

Preprocessing includes energy minimization and position-restrained dynamics. 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

As shown in Step 5 above, after the final production run is complete, Molecular Lab generates the following outputs:

*1. GRO, TOP, and MDP files, which may be used to repeat the same simulation with different MDP parameters. By skipping the solvate step, the user may run simulations without going through the entire Molecular Lab process.

*2. Initial and final configuration images.

*3. Trajectory files in a PDB format.

*4. 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.

In the future, more output options and advanced visualization tools will be available. Current powerful visualization tools we recommend are PyMOL and Visual Molecular Dynamics (VMD). The user may download the PDB file and use PyMOL (http://pymol.sourceforge.net/) or VMD (http://www.ks.uiuc.edu/Research/vmd/) to visualize the molecule's trajectory. The example below contains an image rendered through VMD.



Example: Hepatitis C Virus protein-membrane anchor

1. Download the PDB file of the protein-membrane anchor of the hepatitis C virus from http://www.rcsb.org/pdb/explore.do?structureId=1R7E.

2. Follow option guidlines below.

PDB and MDP
SituationHave the input pdb file
Uploading the MoleculesUpload
Position restrained mdrun?Yes
Have MDP file?No
Box generation and Energy minimization
Force field type for pdb2gmxoplsaa OPLS-AA/L all-atom force field
mdp file parameters
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 typeBerendsen
GroupsPROTEIN
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
Preprocessing only
Include in production run?Yes

3. Click Simulate and wait for about 5 minutes for simulation to run.

4. After simulation completes, download the output .trr file and input it into a graphics program like VMD or Pymol. The following is a post-simulation image created by VMD.

Contributors

ContributornanoHUB login Institution
Kazutora HayashidahayaskaStanford University
Artit WangperawongartitwStanford University
Eric DarvedarveStanford University