We wish to gratefully acknowledge the original inspiration and extensive support provided to us toward the creation of this system from Dr. Oliver Kreylos of the UC Davis Institute for Data Analysis and Visualization. His advice and assistance were instrumental to our success.
We also wish to thank the NSF BRIGE program for providing funding for this project. This material is based upon work supported by the National Science Foundation under Grant No. 1032653.

1. Install 3D/VR Modeling Software on Modeling PC
<ol>
	<li>Install LINUX base operating system on modeling PC (Ubuntu x86 / AMD64 depending on hardware).</li>
	<li>Modify LINUX base operating system.
	<ol>
		<li>Install libraries and add functionality as necessary.</li>
	</ol>
	</li>
	<li>Install VRUI and NCK 3D/VR modeling software on Modeling PC6.
	<ol>
		<li>Check related websites1,6 to obtain latest versions of all modeling software components.</li>
		<li>Compile, configure and test VRUI.</li>
		<li>Install and test NCK.</li>
	</ol>
	</li>
</ol>
2. Set Up Tracking System1
<ol>
	<li>Mount IR Tracking Cameras4
	<ol>
		<li>Create a rigid camera suspension frame directly above the front edge of the 3D TV near the ceiling for best coverage. Mount 3 cameras on swivel mounts directly above the front corners and the front center of the 3D TV. Ensure that the coverage angle of each camera just grazes the front surface of the TV.</li>
		<li>Aim the cameras to have the widest coverage angle (45 degrees) parallel to the front of the 3D TV. Use a narrower coverage angle (30 degrees) perpendicular to the front of the 3D TV. Allow for maximum overlap within the desired 3D working space. Ensure objects are in view of at least two cameras to be tracked successfully (Figure 3). 
		<img alt="Figure 3" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig3highres.jpg" width="500" /> 
		Figure 3. IR tracking camera coverage to maximize 3D workspace in front of TV. Parts (A) and (B) show front and side view with respect of the 3D/VR Visualization System. <a href="https://www.jove.com/files/ftp_upload/51384/51384fig3highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a></li>
	</ol>
	</li>
	<li>Experiment with alternate camera placement if required to create an adequate 3D workspace. This may be required if the vertical camera mounting distance is constrained.</li>
	<li>Install and Calibrate Tracking Software
	<ol>
		<li>Install the OptiTrack Rigid Body Toolkit on the tracking computer using included installation manual.</li>
		<li>Set Threshold, Exposure, Illumination values dependent on environment and set the Capture Quality to high, as detailed in the tracking software instructions.</li>
		<li>For the Wand Capture, be careful to remove all other reflective material from the 3D workspace. Move smoothly throughout camera overlap working area with the reflective wand. Repeat until standard and mean errors below &#8220;0.5&#8221; are obtained then save the calibration file.</li>
		<li>Set the ground plane to establish a tracked 3D work area coordinate system origin. Define the Wiimote and 3D goggle tracked objects as detailed in the tracking software instructions.</li>
	</ol>
	</li>
	<li>Complete VRUI Calibration
	<ol>
		<li>Set VRUI to accept tracking information from tracking computer.</li>
		<li>Verify tracking functionality in VRUI using DeviceTest calibration utility.</li>
		<li>Align VRUI 3D display and tracking software coordinate systems.</li>
		<li>Set orientation of tracked Wiimote and 3D goggles using AlignTrackingMarkers alignment software.</li>
	</ol>
	</li>
</ol>
3. Prepare 3D Modeling System for Use
<ol>
	<li>Before beginning, remove all reflective jewelry (i.e., watches, earrings, metals, etc.). Do not remove corrective glasses needed to focus on the screen.</li>
	<li>Assemble the equipment for the 3D/VR Visualization System:
	<ol>
		<li>Modeling computer</li>
		<li>Tracking computer</li>
		<li>Large format 3D-capable TV</li>
		<li>Video cable between modeling computer and 3D TV</li>
		<li>3D IR emitter for 3D TV</li>
		<li>Ethernet cables for modeling and tracking computers</li>
		<li>Wiimote with tracking antlers (controller)</li>
		<li>3D goggles with tracking antlers (3D goggles)5</li>
	</ol>
	</li>
	<li>Carefully place controller where it can be reached easily from modeling computer, taking care not to touch or move the spherical IR tracking markers attached to it.</li>
	<li>Carefully place 3D goggles on TV stand (as before, be sure to avoid touching the reflective markers).</li>
	<li>Connect the three USB cables from the IR cameras mounted above the 3D TV to 3 USB ports on the tracking computer, while it is powered OFF.</li>
	<li>Locate the 3D TV remote control and place it in front of 3D TV.</li>
	<li>Connect the video cable to the video card on the modeling computer and the video input of the 3D TV. Also connect the 3D IR emitter for the 3D synchronizing output from the 3D TV, and place emitter on TV stand near side of TV, pointing up toward where goggles will be used. BE VERY CAREFUL NOT to shift the position of the calibrated TV.</li>
	<li>Turn 3D TV ON before powering on the modeling computer to ensure proper recognition by the computer.</li>
	<li>Turn ON modeling computer. After the modeling computer boots to a login prompt, log in on the modeling computer LINUX system to an appropriate account.</li>
	<li>Once the modeling computer desktop is available, use the 3D TV remote control to check the status of the video cable connection by pressing the &#8220;info/i&#8221; button. Ensure that the TV screen displays &#8220;1920x1080 @ 60hz&#8221; in the upper left corner. If not, reboot the modeling computer to establish correct recognition of the 3D TV. Also be sure TV is in 3D output MODE 2, using the remote control setup menus.</li>
	<li>On the modeling computer desktop, open a terminal window with several tabs.</li>
	<li>On the tracking computer, verify the ethernet adapter IP address by typing &#8220;ipconfig&#8221; in a command window.</li>
	<li>On the modeling computer, open a terminal window tab and check within the VRDevices.cfg file that the &#8220;serverName&#8221; defines the tracking computer ethernet adapter IP address.</li>
	<li>If necessary, alter the &#8220;serverName&#8221; IP address in VRDevices.cfg to match the tracking computer ethernet adapter, and save VRDevices.cfg.</li>
	<li>On the tracking computer, initiate the OptiTrack Rigid Body Tool software.</li>
	<li>Allow the software to open completely, then click the large button near the top menu labeled &#8220;Load Calibration Result&#8221;.</li>
	<li>Browse to and open the appropriate camera calibration file.</li>
	<li>After the file is loaded, click the &#8220;File&#8221; menu and select &#8220;Load rigid body definitions&#8221;.</li>
	<li>Browse to and open the appropriate rigid body definition file for the tracked controller and 3D goggles.</li>
	<li>On the rightmost pane of the tracking software, locate the section labeled &#8220;Streaming&#8221;, expand the section and under the &#8220;VRPN Streaming&#8221; category, verify that the port number listed is 3883, then check the &#8220;Broadcast frame data&#8221; box inside the &#8220;VRPN Streaming Engine&#8221; category.</li>
	<li>At the modeling computer, make sure that the controller is either directly in hand or immediately reachable (2 sec away at the most).</li>
	<li>On the modeling computer, bring up a tab in the terminal window created earlier in this session and navigate to and then initiate the VRDeviceDaemon software, e.g., typing &#8220;./VRDeviceDaemon&#8221;.</li>
	<li>Follow the prompt to &#8220;press buttons 1 &#38; 2 on the Wiimote simultaneously.&#8221; If the activity was successful, the window will now display &#8220;VRDeviceServer: Waiting for client connection&#8221;.</li>
</ol>
4. Test 3D/VR Visualization System Using NCK Software
The following set of instructions outlines how to use the NCK software on-screen menus to establish controller tool functions, and then how to build and manipulate a carbon nanotube in the 3D/VR workspace from constituent carbon atoms (Figure 4). Instructions on how to measure the resulting bond angles and distances (Step 4.4.10) are available online10.
<img alt="Figure 4" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig4highres.jpg" width="500" /> 
Figure 4. Undergraduate student using the 3D/VR Visualization System to study carbon nanotubes (CNTs). Photos (A)-(F) show the building process of a single-walled CNT. <a href="https://www.jove.com/files/ftp_upload/51384/51384fig4highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol>
	<li>Within the modeling computer terminal window created in Step 3.11, select the third tab.&#160; To initiate the NCK software, navigate to the NCK installation directory and type: 
	&#8220;./NanotechConstructionKit -rootSection localhost -domainsize 36&#8221;.</li>
	<li>Being very careful not to touch or loosen the attached tracking markers, put on 3D goggles and pick up the controller. Adjust head/goggle viewing position to ensure 3D goggles are receiving 3D TV IR emitter sync signal, allowing 3D/VR viewing of TV display.</li>
	<li>In order to have a toolset to add, move and delete atoms, assign NCK command associations to buttons on the controller as follows:
	<ol>
		<li>Bring up the main NCK on-screen menu by pressing and holding the Home button on the Wiimote, navigating to and selecting the &#8220;Override Tools&#8221; menu item, then releasing the Home button. This allows assignment of commands to different buttons on the controller independently of one another.</li>
		<li>To associate the Wiimote trigger button (on the bottom of the controller) with the action of manipulating atoms within NCK, press and hold the trigger button, navigate the on-screen NCK menu to &#8220;Dragger&#8221; and select &#8220;6-DOF Dragger,&#8221; then release the trigger. The trigger is now associated with the action of manipulating the atoms.</li>
		<li>To assign the function of adding an atom to the &#8220;+&#8221; button on the Wiimote, bring the main menu up by pressing and holding the Home button, navigate to &#8220;Structural Unit Types&#8221;, and select &#8220;Triangle&#8221;, then release the Home button.</li>
		<li>Next press and hold the &#8220;+&#8221; button, navigate to &#8220;Dragger,&#8221; and select &#8220;6-DOF Dragger,&#8221; then release the &#8220;+&#8221; button. The &#8220;+&#8221; button is now associated with creating new atoms of the type selected (carbon atoms represented by triangles, in this case).</li>
		<li>To assign the function of deleting an atom to the &#8220;-&#8221; button on the Wiimote, bring up the main menu by pressing and holding the &#8220;Home&#8221; button, then navigate to &#8220;Structural Unit Types,&#8221; and select &#8220;Delete Selected Units,&#8221; then release the Home button.</li>
		<li>Next, press and hold the &#8220;-&#8221; button, navigate to &#8220;Dragger,&#8221; then &#8220;6-DOF Dragger,&#8221; and release the &#8220;-&#8220; button. The &#8220;-&#8221; button is now associated with deleting atoms.</li>
		<li>Follow a similar procedure to assign the functions of &#8220;Lock Selected Units&#8221; to the &#8220;1&#8221; Wiimote button, and &#8220;Unlock Selected Units&#8221; to the &#8220;2&#8221; controller button.</li>
	</ol>
	</li>
	<li>Once the controller buttons have been configured, create a carbon nanotube using NCK as follows:
	<ol>
		<li>Using the &#8220;+&#8221; button, add two 3-bond triangular carbon atoms to the NCK workspace. Manipulate these using the trigger button until they join at a vertex.</li>
		<li>Add 4 more carbon atoms to create a hexagonal star shape.</li>
		<li>Using the &#8220;Home&#8221; menu, navigate to &#8220;I/O Menus&#8221;, then &#8220;Save Units .</li>
		<li>Move the 6 pointed structure away from its current position.</li>
		<li>Using the &#8220;Home&#8221; menu, navigate to &#8220;I/O Menus&#8221;, then &#8220;Load Units .</li>
		<li>Repeat the last 2 steps until a 6 by 6 sheet of hexagonal 6-atom rings has been created (Figure 5A).</li>
		<li>Using the &#8220;1&#8221; button, lock one atom in the top row, and an opposing atom in the bottom row. The locked atoms will be marked with a pink color (Figure 5B).</li>
		<li>Using the trigger button, carefully move one of the locked atoms in a circular arc until its free vertex approaches the free vertex of the opposing locked atom. A green line will appear between the vertices when they are close enough that atomic attraction will cause them to join with a bond (Figure 5C). Once successfully joined, unlock both of the atoms using the &#8220;2&#8221; button.</li>
		<li>Continue similarly locking, joining, and unlocking opposing atomic vertices in the carbon sheet, effectively &#8220;zipping&#8221; the sheet into a final carbon nanotube (Figures 5D-5F). 
		<img alt="Figure 5" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig5highres.jpg" width="500" /> 
		Figure 5. Step-wise creation of a single-walled CNT showing (A) a 6 x 6 sheet (graphene) of hexagonal carbon rings, (B) opposing carbon atoms &#8220;locked&#8221; (shown as pink triangles) to allow easier manipulation against realistic interatomic forces, (C) carbon (graphene) sheet carefully curved to allow bonding between atoms on opposing sides, (D) two additional opposing carbon atoms locked to assist further carbon sheet curvature, (E) additional opposing carbon atoms bonded to continue carbon sheet curvature into a nanotube, and (F) final CNT formed after sequential bonding of opposing atoms of the original carbon sheet (graphene). <a href="https://www.jove.com/files/ftp_upload/51384/51384fig5highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a></li>
		<li>When the nanotube is complete, use on-screen measurement tools to confirm structural angles and distances10.</li>
	</ol>
	</li>
</ol>
5. Visualization of Molecular Dynamics Simulation Models
<ol>
	<li>Import an initial crystalline SiO2 cubical model into the 3D/VR NCK software, and investigate the initial structure (see Figure 2A).</li>
	<li>Open-source programs MDCASK11 and LAMMPS12 were targeted because of features that are well-suited to this research focus. The latter program is used in this work given its varied interatomic potentials and GPU computing capability. Using the LAMMPS MD package12, run a simulated melt/quench procedure on this initial structure to produce an amorphous SiO2 structure. Details on this simulated procedure can be found in previous publications13-15.</li>
	<li>Import the resulting new amorphous (disordered) SiO2 model into the 3D/VR NCK software and investigate the structure (see Figure 2B).</li>
	<li>Create a SiO2 nanospring/nanoribbon out of the new amorphous solid using the open source code NanospringCarver16 and associated instructional documentation17 (Figure 6). <img alt="Figure 6" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig6highres.jpg" width="500" /> 
	Figure 6. Illustration of the step-by-step atom selection process at different stages in the creation of a nanospring using the NanospringCarver program. Parts (A-D) indicate 25%, 50%, 75% and 100% completion of this process17. <a href="https://www.jove.com/files/ftp_upload/51384/51384fig6highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a></li>
	<li>Use the LAMMPS MD package to perform tensile simulations on the nanospring/nanoribbon (Figure 7). Details on this procedure can be found in a previous publication15. 
	<img alt="Figure 7" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig7highres.jpg" width="500" /> 
	Figure 7. Snapshot image from LAMMPS MD silica helical nanostructure (nanoribbon) tensile simulation results.</li>
	<li>Use the open source software tools VMD (Visualize Molecular Dynamics)18 ImageMagick19, and FFmpeg20 to create snapshots and animation of the helical nanostructure throughout this simulation (Animated Figure 1), for presentation in the 3D/VR Visualization System. <a href="https://www.jove.com/files/ftp_upload/51384/51384fig7highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a></li>
</ol>
<a href="https://www.jove.com/files/ftp_upload/51384/Animated_Fig1-movie NR-0140_frames.mov" target="_blank">Animated Figure 1</a>. Animation of helical nanostructure tensile simulation.

<ol>
	<li>Doblack, B. N., Flores, C., Matlock, T., D&#225;vila, L. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+emergence+of+immersive+low-cost+3D+virtual+reality+environments+for+interactive+learning+in+materials+science+and+engineering.">The emergence of immersive low-cost 3D virtual reality environments for interactive learning in materials science and engineering.</a> Mater. Res. Soc. Symp. Proc. 1320, (2011).</li><li>Flores, C., Matlock, T., D&#225;vila, L. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhancing+materials+research+through+innovative+3D+environments+and+interactive+manuals+for+data+visualization+and+analysis.">Enhancing materials research through innovative 3D environments and interactive manuals for data visualization and analysis.</a> Mater. Res. Soc. Symp. Proc. 1472, (2012).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D+goggle+source.">3D goggle source.</a> , (2013).</li><li>. &#8220;3D/VR Visualization System - Startup and Shutdown Protocol&#8221; and &#8220;3D/VR Visualization System &#8211; CNT Modeling Example&#8221; documents Available from: <a target="_blank" href="https://eng.ucmerced.edu/people/ldavila/home/3d-vr-visualization-system-dissemination-of-research-results-and-products">https://eng.ucmerced.edu/people/ldavila/home/3d-vr-visualization-system-dissemination-of-research-results-and-products</a> (2013)</li><li>. MDCASK molecular dynamics code Available from: <a target="_blank" href="https://asc.llnl.gov/computing_resources/purple/archive/benchmarks/mdcask">https://asc.llnl.gov/computing_resources/purple/archive/benchmarks/mdcask</a> (2013)</li><li>Feuston, B. P., Garofalini, S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Empirical+three-body+potential+for+vitreous+silica.">Empirical three-body potential for vitreous silica.</a> J. Chem. Phys. 89 (9), 5818-5824 (1988).</li><li>D&#225;vila, L. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transformations+in+the+medium-range+order+of+fused+silica+under+high+pressure.">Transformations in the medium-range order of fused silica under high pressure.</a> Phys. Rev. Lett. 91 (20), 2055011-2055014 (2003).</li><li>Doblack, B. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The structure and properties of silica glass nanostructures using novel computational systems. , (2013).</li><li>Meagher, K. A., Doblack, B. N., Ramirez, M., D&#225;vila, L. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scalable+nanohelices+for+predictive+studies+and+enhanced+3D+visualization.">Scalable nanohelices for predictive studies and enhanced 3D visualization.</a> J. Vis. Exp. In-Press, .</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=University+of+California+Television+(UCTV).">University of California Television (UCTV).</a> Our Digital Life series: The Future: Teaching and Life-Saving Tools episode. , (2013).</li></ol>

The authors declare that they have no competing financial interests.

Critical elements in the successful installation and usage of the 3D/VR Visualization System are detailed in the Physical Environment and Design Considerations and Special Considerations in supplemental materials. Important installation considerations include 3D display height for comfortable long-term standing or seated usage, maximized tracking camera mounted height to create a large 3D working area, stable tracking camera and 3D display support to maintain configuration over time, and...

Materials science is an interdisciplinary field that examines the structure-property relationships in matter for their application to many areas of science and engineering. As structure-property relationships are investigated through computer simulations in addition to experimentation, computational tools offer complementary features that can enhance research efforts. While nanomaterials are of interest to scientists and have redeeming value for their potential social impact, this size regime is fraught with many challenges found particularly in experimentation.
Computer simulations allow scientists and engineers to perform specialized tests in a large variety of environments limited only by time and computational resources. Molecular dynamics (MD) simulations allow the appropriate time and length scales to study the phenomena of interest in many nanomaterials. Simulations expand the study of materials by removing the constraints of the physical laboratory, however many computational tools lack accessible, intuitive interfaces for research. Enhancement with the graphical display of models, efficient computational algorithms, and graphical processing unit (GPU) based computing complement current simulation efforts. These new graphics devices combine with central processing units efficiently to allow mathematically intensive calculations to be accomplished by the GPU. The result is an effective acceleration of computation on the order of 10x accompanied by a reduction in power consumption of up to 20x.
The goal of this research project was to develop and implement a novel tool for nanoscience investigation that directly connects an interactive interface to MD simulations, materials science analysis and 3D visualization. This innovative system with unique and powerful analysis capabilities has been used for nanoscale research and education at UC Merced, with direct implications to other related STEM fields such as nanotechnology, physics, biology, and geology, and ultimate benefit to education and society.
The 3D/VR Visualization System was implemented as both a research and teaching instrument which allows creation and manipulation of atomic structures in an interactive 3D virtual reality (VR) environment. The system was created from a set of relatively low-cost and accessible components following the model originally developed by Dr. Oliver Kreylos at UC Davis1.
Below is a photo of the final 3D/VR Visualization System layout, with important components labeled (Figure 1). This system was originally established for education purposes at UC Merced in 2009. The implementation of the original 3D/VR system resulted in peer-reviewed publications2-3. Table 1 below summarizes key characteristics for each element of the 3D/VR Visualization System.
<img alt="Figure 1" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig1highres.jpg" width="500" /> 
Figure 1. 3D/VR Visualization System and main components (left) in the Davila Research Laboratory at UCM and visualization devices (right). <a href="https://www.jove.com/files/ftp_upload/51384/51384fig1highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Item</td>
			<td>Component</td>
			<td>Functionality in System</td>
		</tr>
		<tr>
			<td>A</td>
			<td>3D TV</td>
			<td>3D display of modeled molecular structures and on-screen menus.</td>
		</tr>
		<tr>
			<td>B</td>
			<td>Infrared (IR) tracking cameras4</td>
			<td>IR cameras track positions of the Wiimote and 3D viewing goggles in the user workspace in front of 3D TV, allowing virtual 3D manipulation of displayed structures.</td>
		</tr>
		<tr>
			<td>C</td>
			<td>Tracking PC</td>
			<td>Runs IR camera tracking software and transmits Wiimote and 3D goggle positions to modeling computer.</td>
		</tr>
		<tr>
			<td>D</td>
			<td>Wiimote</td>
			<td>Used for on-screen management of modeling software and to manipulate structures in 3D virtual environment.</td>
		</tr>
		<tr>
			<td>E</td>
			<td>3D goggles5</td>
			<td>Synchronized with 3D TV IR signal, allow 3D view of structure. Position tracked by IR cameras for accurate 3D view.</td>
		</tr>
		<tr>
			<td>F</td>
			<td>Modeling PC</td>
			<td>Runs NCK/VRUI 3D modeling and display software6, accepts goggle / Wiimote position and control signals to create accurate 3D molecular structure view.</td>
		</tr>
	</tbody>
</table>
Table 1. Functionality of main elements of the 3D/VR Visualization System at UCM.
Description of 3D/VR Visualization System and Basic Components:
3D/VR Visualization System Overview &#8212; The 3D/VR Visualization System consists of a set of IR cameras and tracking software operating in conjunction with 3D modeling software to allow a user to interactively create 3D molecular structures. The IR cameras and software track the 3D location of a Wiimote and 3D viewing goggles using IR markers, and pass this to the modeling software. The modeling software uses the Wiimote control signals and movement to generate 3D molecular structures viewable using the combination of a 3D-capable large format television with synchronized and tracked 3D goggles. This results in a 3D virtual reality workspace within which the user can dynamically create and manipulate virtual molecular structures which reflect real-world physical behavior based on inter-atomic forces used in the modeling software (Figure 2). Special considerations for setting up this system can be found in supplemental materials.
<img alt="Figure 2" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig2highres.jpg" width="500" /> 
Figure 2. Investigating silica nanomaterials using the 3D/VR Visualization System. (a) A researcher creates an initial cristobalite model (crystalline) before GPU-based simulations. (b) Upon performing a simulated MD melt-quench procedure on model shown in (a), another researcher obtains a silica glass model (non-crystalline). <a href="https://www.jove.com/files/ftp_upload/51384/51384fig2highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
3D/VR Visualization System Enhancement &#8212; MD Simulation Capability:
Molecular dynamics simulation systems are commonly implemented in a multi-nodal fashion, that is, a large workload is distributed or parallelized among tens to thousands of processors. Recently, additional opportunities for accelerated scientific computing have arisen out of developments in computer graphics processing. These advances include a software interface allowing scientists to take advantage of the highly parallel nature of the processing power intrinsic to graphics chips. With the advent of the Compute Unified Device Architecture or CUDA7, scientists can use GPUs8 to enhance the speed at which problems are solved while reducing the cost of infrastructure. A typical GPU may have the equivalent of hundreds to thousands of cores or &#8220;nodes&#8221; for processing information, and as these can each be used in parallel, a well-coded solution may provide up to 1,000x throughput acceleration against its multi-core counterpart. Though not every problem is well-suited to this approach, current MD simulations have seen up to 15x throughput performance gains9. Details on the 3D/VR visualization system MD-GPU enhancement can be found in supplemental materials.

<table><tbody><tr><td>Samsung 61&quot; 3D-capable high definition DLP TV</td><td>Samsung</td><td>&lt;a href=&quot;http://www.samsung.com/us/video/tvs&quot;&gt;http://www.samsung.com/us/video/tvs&lt;/a&gt;</td><td>See Protocol Section 3 (Step 3.2)&amp;nbsp; (Large format 3D-capable TV)</td></tr><tr><td>Alienware Area51 750i modeling computer</td><td>Alienware</td><td>&lt;a href=&quot;http://www.alienware.com/&quot;&gt;http://www.alienware.com&lt;/a&gt;</td><td>See Protocol Section 1 (Step 1.1)&amp;nbsp; (Modeling computer)</td></tr><tr><td>HP EliteBook 8530w tracking computer</td><td>HP</td><td>&lt;a href=&quot;http://www.hp.com/&quot;&gt;http://www.hp.com&lt;/a&gt;</td><td>See Protocol Section 2 (Step 2.3)&amp;nbsp; (Tracking computer)</td></tr><tr><td>V100:R2 IR tracking cameras (3)</td><td>Naturalpoint</td><td>&lt;a href=&quot;http://www.naturalpoint.com/optitrack/products/v100-r2/&quot;&gt;http://www.naturalpoint.com/optitrack/products/v100-r2/&lt;/a&gt;</td><td>See Protocol Section 2 (Step 2.1) and Reference [4]&amp;nbsp; (Tracking cameras)</td></tr><tr><td>OptiTrack Tracking Tools IR tracking software</td><td>Naturalpoint</td><td>&lt;a href=&quot;http://www.naturalpoint.com/optitrack/software/&quot;&gt;http://www.naturalpoint.com/optitrack/software/&lt;/a&gt;</td><td>See Protocol Section 2 (Step 2.3) and Reference [4]&amp;nbsp; (Tracking software)</td></tr><tr><td>3D Goggles and 3D TV IR sync emitter</td><td>Ilixco</td><td>&lt;a href=&quot;http://www.i-glassesstore.com/dlp3d-wireless-2set.html&quot;&gt;http://www.i-glassesstore.com/dlp3d-wireless-2set.html&lt;/a&gt;</td><td>See Protocol Section 3 (Step 3.2) and Reference [5]&amp;nbsp; (3D goggles)</td></tr><tr><td>Wiimote 3D controller</td><td>Nintendo</td><td>&lt;a href=&quot;http://www.nintendo.com/wii&quot;&gt;http://www.nintendo.com/wii&lt;/a&gt;</td><td>See Protocol Section 3 (Step 3.2)&amp;nbsp; (Wiimote)</td></tr><tr><td>VRUI, NCK and associated 3D/VR modeling software</td><td>Open source software</td><td>&lt;a href=&quot;http://idav.ucdavis.edu/~okreylos/ResDev/NanoTech/index.html&quot;&gt;http://idav.ucdavis.edu/~okreylos/ResDev/NanoTech/index.html&lt;/a&gt;</td><td>See Protocol Section 1 (Step 1.3) and References [1,6]&amp;nbsp; (VRUI, NCK)</td></tr><tr><td>LAMMPS molecular dynamics software</td><td>Open source software</td><td>&lt;a href=&quot;http://lammps.sandia.gov/&quot;&gt;http://lammps.sandia.gov/&amp;nbsp;&lt;/a&gt;</td><td>See Protocol Section 5 (Step 5.2) and Reference [12]&amp;nbsp; (LAMMPS)</td></tr><tr><td>NanospringCarver program code and files</td><td>UC Merced - open source</td><td>&lt;a href=&quot;http://tinyurl.com/qame8dj&quot;&gt;http://tinyurl.com/qame8dj&lt;/a&gt;</td><td>See Protocol Section 5 (Step 5.4) and References [16-17]&amp;nbsp; (NanospringCarver)</td></tr><tr><td>MATLAB GUI files</td><td>UC Merced - open source</td><td>&lt;a href=&quot;http://tinyurl.com/qame8dj&quot;&gt;http://tinyurl.com/qame8dj&lt;/a&gt;</td><td>See Protocol Section 5 (Step 5.4) and References [16-17]&amp;nbsp; (NanospringCarver)</td></tr><tr><td>Atomistic bulk glass input file</td><td>UC Merced - open source</td><td>&lt;a href=&quot;http://tinyurl.com/qame8dj&quot;&gt;http://tinyurl.com/qame8dj&lt;/a&gt;</td><td>See Protocol Section 5 (Step 5.4) and References [16-17]&amp;nbsp; (NanospringCarver)</td></tr></tbody></table>

novel 3d/vr interactive environment for md simulations, visualization and analysis

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

This 3D/VR Visualization System presents new opportunities for conducting materials science studies. As this immersive environment operates in real time, in the form of 3D input and display, the researcher is presented with a fully interactive nanoscaled instrument2. By following the protocol presented here, a silica helical nanoribbon was created in this step-by-step fashion. A snapshot of this structure produced from LAMMPS MD is shown in Figure 7. This structure was subjected to simulated t...

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Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

A new computational system featuring GPU-accelerated molecular dynamics simulation and 3D/VR visualization, analysis and manipulation of nanostructures has been implemented, representing a novel approach to advance materials research and promote innovative investigation and alternative methods to learn about material structures with dimensions invisible to the human eye.

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials ...

novel-3dvr-interactive-environment-for-md-simulations-visualization

Research

JoVE Journal

Engineering

11.8K Views.  University of California Merced. A new computational system featuring GPU-accelerated molecular dynamics simulation and 3D/VR visualization, analysis and manipulation of nanostructures has been implemented, representing a novel approach to advance materials research and promote innovative investigation and alternative methods to learn about material structures with dimensions invisible to the human eye.

Video: Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Human Fear Conditioning Conducted in Full Immersion 3-Dimensional Virtual Reality 

Fear conditioning is a widely used paradigm in non-human animal research to investigate the neural mechanisms underlying fear and anxiety. A major challenge in conducting conditioning studies in humans is the ability to strongly manipulate or simulate the environmental contexts that are associated with conditioned emotional behaviors. In this regard, virtual reality (VR) technology is a promising tool. Yet, adapting this technology to meet experimental constraints requires special accommodations. Here we address the methodological issues involved when conducting fear conditioning in a fully immersive 6-sided VR environment and present fear conditioning data.
In the real world, traumatic events occur in complex environments that are made up of many cues, engaging all of our sensory modalities. For example, cues that form the environmental configuration include not only visual elements, but aural, olfactory, and even tactile. In rodent studies of fear conditioning animals are fully immersed in a context that is rich with novel visual, tactile and olfactory cues. However, standard laboratory tests of fear conditioning in humans are typically conducted in a nondescript room in front of a flat or 2D computer screen and do not replicate the complexity of real world experiences. On the other hand, a major limitation of clinical studies aimed at reducing (extinguishing) fear and preventing relapse in anxiety disorders is that treatment occurs after participants have acquired a fear in an uncontrolled and largely unknown context. Thus the experimenters are left without information about the duration of exposure, the true nature of the stimulus, and associated background cues in the environment1. In the absence of this information it can be difficult to truly extinguish a fear that is both cue and context-dependent. Virtual reality environments address these issues by providing the complexity of the real world, and at the same time allowing experimenters to constrain fear conditioning and extinction parameters to yield empirical data that can suggest better treatment options and/or analyze mechanistic hypotheses.
In order to test the hypothesis that fear conditioning may be richly encoded and context specific when conducted in a fully immersive environment, we developed distinct virtual reality 3-D contexts in which participants experienced fear conditioning to virtual snakes or spiders. Auditory cues co-occurred with the CS in order to further evoke orienting responses and a feeling of "presence" in subjects 2 . Skin conductance response served as the dependent measure of fear acquisition, memory retention and extinction.

Human Fear Conditioning Conducted in Full Immersion 3-Dimensional Virtual Reality

Classical fear conditioning paradigm was adapted for human participants in a fully immersive virtual reality setting. Using a discrimination paradigm, conditioned fear, cue and context memory retention, and extinction was measured with skin conductance response to dynamic virtual snakes and spiders (the conditioned stimuli) in two distinct virtual contexts.

Fear conditioning is a widely used paradigm in non-human animal research to investigate the neural mechanisms underlying fear and anxiety. A major ...

Neuroscience

Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications.&#160; For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately.&#160; To study the effect of local structure on the properties of these complex geometries one must develop realistic models.&#160; To date, software packages are rather limited in creating atomistic helical models.&#160; This work focuses on producing atomistic models of silica glass (SiO2) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of &#8220;bulk&#8221; silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented.&#160; The first method employs the AWK programming language and open-source software to effectively carve various shapes of silica nanoribbons from the initial bulk model, using desired dimensions and parametric equations to define a helix.&#160; With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions.&#160; The second method involves a more robust code which allows flexibility in modeling nanohelical structures.&#160; This approach utilizes a C++ code particularly written to implement pre-screening methods as well as the mathematical equations for a helix, resulting in greater precision and efficiency when creating nanospring models.&#160; Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created.&#160; An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material.&#160; In addition, a MATLAB graphical user interface (GUI) is used to enhance learning through visualization and interaction for a general user with the atomistic helical structures.&#160; One application of these methods is the recent study of nanohelices via MD simulations for mechanical energy harvesting purposes.

Accurate modeling of nanohelical structures is important for predictive simulation studies leading to novel nanotechnology applications.&#160; Currently, software packages and codes are limited in creating atomistic helical models.&#160; We present two procedures designed to create atomistic nanohelical models for simulations, and a graphical interface to enhance research through visualization.

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing ...

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis. This integrated functionality provides a complete online workflow for investigating sequence-structure-dynamic relationships within protein families and superfamilies.

A protocol for the online investigation of protein sequence-structure-dynamics relationships using Bio3D-web is presented.

We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality ...

Biochemistry

Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface

Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building blocks in a bottom-up approach is still open. The scanning probe microscope (SPM) could be a tool of choice; however, SPM-based manipulation was until recently limited to two dimensions (2D). Binding the SPM tip to a molecule at a well-defined position opens an opportunity of controlled manipulation in 3D space. Unfortunately, 3D manipulation is largely incompatible with the typical 2D-paradigm of viewing and generating SPM data on a computer. For intuitive and efficient manipulation we therefore couple a low-temperature non-contact atomic force/scanning tunneling microscope (LT NC-AFM/STM) to a motion capture system and fully immersive virtual reality goggles. This setup permits &#34;hand controlled manipulation&#34; (HCM), in which the SPM tip is moved according to the motion of the experimenter&#39;s hand, while the tip trajectories as well as the response of the SPM junction are visualized in 3D. HCM paves the way to the development of complex manipulation protocols, potentially leading to a better fundamental understanding of nanoscale interactions acting between molecules on surfaces. Here we describe the setup and the steps needed to achieve successful hand-controlled molecular manipulation within the virtual reality environment.

We demonstrate the precise manipulation of individual organic molecules on a metal surface with the tip of a scanning probe microscope driven in 3D by the experimenter's hand using a motion capture system and fully immersive virtual reality goggles.

Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building ...

MPI CyberMotion Simulator: Implementation of a Novel Motion Simulator to Investigate Multisensory Path Integration in Three Dimensions

Path integration is a process in which self-motion is integrated over time to obtain an estimate of one's current position relative to a starting point 1. Humans can do path integration based exclusively on visual 2-3, auditory 4, or inertial cues 5. However, with multiple cues present, inertial cues - particularly kinaesthetic - seem to dominate 6-7. In the absence of vision, humans tend to overestimate short distances (&lt;5 m) and turning angles (&lt;30&deg;), but underestimate longer ones 5. Movement through physical space therefore does not seem to be accurately represented by the brain.
Extensive work has been done on evaluating path integration in the horizontal plane, but little is known about vertical movement (see 3 for virtual movement from vision alone). One reason for this is that traditional motion simulators have a small range of motion restricted mainly to the horizontal plane. Here we take advantage of a motion simulator 8-9 with a large range of motion to assess whether path integration is similar between horizontal and vertical planes. The relative contributions of inertial and visual cues for path navigation were also assessed.
16 observers sat upright in a seat mounted to the flange of a modified KUKA anthropomorphic robot arm. Sensory information was manipulated by providing visual (optic flow, limited lifetime star field), vestibular-kinaesthetic (passive self motion with eyes closed), or visual and vestibular-kinaesthetic motion cues. Movement trajectories in the horizontal, sagittal and frontal planes consisted of two segment lengths (1st: 0.4 m, 2nd: 1 m; &plusmn;0.24 m/s2 peak acceleration). The angle of the two segments was either 45&deg; or 90&deg;. Observers pointed back to their origin by moving an arrow that was superimposed on an avatar presented on the screen.
Observers were more likely to underestimate angle size for movement in the horizontal plane compared to the vertical planes. In the frontal plane observers were more likely to overestimate angle size while there was no such bias in the sagittal plane. Finally, observers responded slower when answering based on vestibular-kinaesthetic information alone. Human path integration based on vestibular-kinaesthetic information alone thus takes longer than when visual information is present. That pointing is consistent with underestimating and overestimating the angle one has moved through in the horizontal and vertical planes respectively, suggests that the neural representation of self-motion through space is non-symmetrical which may relate to the fact that humans experience movement mostly within the horizontal plane.

An efficient way to gain insight into how humans navigate themselves in three dimensions is described. The method takes advantage of a motion simulator capable of moving observers in ways unattainable by traditional simulators. Results confirm that movement in the horizontal plane is underestimated, while vertical movement is overestimated.

Path integration is a process in which self-motion is integrated over time to obtain an estimate of one's current position relative to a starting point 1. ...

Interactive Molecular Model Assembly with 3D Printing

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical laboratories and chemical education. Building on the long and successful history of physical modeling of molecular systems, we present select models along with a protocol to facilitate 3D printing of molecular structures that are able to do more than represent shape and connectivity. Models assembled as described incorporate dynamic aspects and degrees of freedom into saturated hydrocarbon structures. As a representative example, cyclohexane was assembled from parts printed and finished using different thermoplastics, and the resulting models retain their functionality at a variety of scales. The resulting structures show configurational space accessibility consistent with calculations and literature, and versions of these structures can be used as aids to illustrate concepts that are difficult to convey in other ways. This exercise enables us to evaluate successful printing protocols, make practical recommendations for assembly, and outline design principles for physical modeling of molecular systems. The provided structures, procedures, and results provide a foundation for individual manufacture and exploration of molecular structure and dynamics with 3D printing.

Physical modeling of microscopic systems helps obtain insights that are difficult to gain by other means. To facilitate the construction of physical molecular models, we demonstrate how 3D printing can be used to assemble functional macroscopic models that capture qualities of molecular systems in a tactile way.

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical ...

Chemistry

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Biomolecular visualization skills are paramount to understanding key concepts in the biological sciences, such as structure-function relationships and molecular interactions. Various programs allow a learner to manipulate 3D structures, and biomolecular modeling promotes active learning, builds computational skills, and bridges the gap between two dimensional textbook images and the three dimensions of life. A critical skill in this area is to model a protein active site, displaying parts of the macromolecule that can interact with a small molecule, or ligand, in a way that shows binding interactions. In this protocol, we describe this process using four freely available macromolecular modeling programs: iCn3D, Jmol/JSmol, PyMOL, and UCSF ChimeraX. This guide is intended for students seeking to learn the basics of a specific program, as well as instructors incorporating biomolecular modeling into their curriculum. The protocol enables the user to model an active site using a specific visualization program, or to sample several of the free programs available. The model chosen for this protocol is human glucokinase, an isoform of the enzyme hexokinase, which catalyzes the first step of glycolysis. The enzyme is bound to one of its substrates, as well as a non-reactive substrate analog, which allows the user to analyze interactions in the catalytic complex.

A key skill in biomolecular modeling is displaying and annotating active sites in proteins. This technique is demonstrated using four popular free programs for macromolecular visualization: iCn3D, Jmol, PyMOL, and UCSF ChimeraX.

Biomolecular visualization skills are paramount to understanding key concepts in the biological sciences, such as structure-function relationships and ...

Visualizing Solution Structure at Solid-Liquid Interfaces using Three-Dimensional Fast Force Mapping

Amongst the challenges for a variety of research fields are the visualization of solid-liquid interfaces and understanding how they are affected by the solution conditions such as ion concentrations, pH, ligands, and trace additives, as well as the underlying crystallography and chemistry. In this context, three-dimensional fast force mapping (3D FFM) has emerged as a promising tool for investigating solution structure at interfaces. This capability is based on atomic force microscopy (AFM) and allows the direct visualization of interfacial regions in three spatial dimensions with sub-nanometer resolution. Here we provide a detailed description of the experimental protocol for acquiring 3D FFM data. The main considerations for optimizing the operating parameters depending on the sample and application are discussed. Moreover, the basic methods for data processing and analysis are discussed, including the transformation of the measured instrument observables into tip-sample force maps that can be linked to the local solution structure. Finally, we shed light on some of the outstanding questions related to 3D FFM data interpretation and how this technique can become a central tool in the repertoire of surface science.

Here, we present a protocol for using three-dimensional fast force mapping - an atomic force microscopy technique - for visualizing solution structure at solid-liquid interfaces with the subnanometer resolution by mapping the tip-sample interactions within the interfacial region.

Amongst the challenges for a variety of research fields are the visualization of solid-liquid interfaces and understanding how they are affected by the ...

A Virtual Simulation Experiment of Mechanics: Material Deformation and Failure Based on Scanning Electron Microscopy

This work presents a set of comprehensive virtual experiments to detect material deformation and failure. The most commonly used pieces of equipment in mechanics and material disciplines, such as a metallographic cutting machine and a high-temperature universal creep testing machine, are integrated into a web-based system to provide different experimental services to users in an immersive and interactive learning environment. The protocol in this work is divided into five subsections, namely, the preparation of the materials, molding the specimen, specimen characterization, specimen loading, nanoindenter installation, and SEM in situ experiments, and this protocol aims to provide an opportunity for users regarding the recognition of different equipment and the corresponding operations, as well as the enhancement of laboratory awareness, etc., using a virtual simulation approach. To provide clear guidance for the experiment, the system highlights the equipment/specimen to be used in the next step and marks the pathway that leads to the equipment with a conspicuous arrow. To mimic the hands-on experiment as closely as possible, we designed and developed a three-dimensional laboratory room, equipment, operations, and experimental procedures. Moreover, the virtual system also considers interactive exercises and registration before using chemicals during the experiment. Incorrect operations are also allowed, resulting in a warning message informing the user. The system can provide interactive and visualized experiments to users at different levels.

This work presents a three-dimensional virtual simulation experiment for material deformation and failure that provides visualized experimental processes. Through a set of experiments, users can become familiar with the equipment and learn the operations in an immersive and interactive learning environment.

This work presents a set of comprehensive virtual experiments to detect material deformation and failure. The most commonly used pieces of equipment in ...

Visual Dynamics: Simplifying Molecular Dynamics Simulations

New Features in Visual Dynamics 3.0

Visual Dynamics (VD) is a web tool that aims to facilitate the use and application of Molecular Dynamics (MD) executed in Gromacs, allowing users without computational familiarity to run short-time simulations for validation, demonstration, and teaching purposes. It is true that quantum methods are the most accurate. However, there is currently no computational feasibility to carry out the experiments that MD performs. The tool described here has continuously received improvements over the course of the last couple of years. This protocol will describe what is needed to run a simulation in VD with a protein-ligand complex previously prepared in ACPYPE and some general directions on the other simulation models available. For the detailed simulation, the FK506-binding protein from Plasmodium vivax complexed with the inhibitor D5 (PDB ID: 4mgv) will be used, and all files used will be provided. Note that this protocol will tell every option to be used to achieve the same results presented, but these options are not necessarily the only ones available.

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Visual Dynamics is an open-source tool that accelerates implementations and learning in molecular dynamics simulation using Gromacs. The presented protocol will guide you through the steps to perform a protein-ligand simulation prepared in ACPYPE with ease and general steps to other simulation models.

Visual Dynamics (VD) is a web tool that aims to facilitate the use and application of Molecular Dynamics (MD) executed in Gromacs, allowing users without ...

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

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Rozdziały w tym wideo

Human Fear Conditioning Conducted in Full Immersion 3-Dimensional Virtual Reality

Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface

MPI CyberMotion Simulator: Implementation of a Novel Motion Simulator to Investigate Multisensory Path Integration in Three Dimensions

Interactive Molecular Model Assembly with 3D Printing

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Visualizing Solution Structure at Solid-Liquid Interfaces using Three-Dimensional Fast Force Mapping

A Virtual Simulation Experiment of Mechanics: Material Deformation and Failure Based on Scanning Electron Microscopy

New Features in Visual Dynamics 3.0