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Teaching enzyme catalysis using interactive molecular dynamics in virtual realitySimon J. Bennie,1,2 Kara E. Ranaghan,1 Helen Deeks,1,2,3 Heather E. Goldsmith, Mike O'Connor,1,2,3 Adrian J. Mulholland,1 and David R. Glowacki1,2,31Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK2Intangible Realities Laboratory, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK 3Dept. of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol, BS8 1UB, UKsimonbennie@; Adrian.Mulholland@bristol.ac.uk;drglowacki@Supporting information containing lab procedure for the study of the binding/unbinding of chorismate with chorismate mutase and the rearrangement of chorismate mutase to prephenate.Setup of hardware:Detailed VR documentation for setting up a room installation of HTC Vive can be found at VR room should be set up with a minimum area of a 3m by 3m square at the centre of the room, the two light-house infrared emitters should be positioned at either the corners of the square on tripods or mounted to the walls of the room. The lab space should have clear markings on the floor to indicate where the boundaries for the VR space will be located so that students outside of the VR environment can recognize the work area. Hardware specificationsWe recommend the HTC Vive pro for teaching activities because of the solid body head band that makes it more robust for repeatedly taking the headset on and off, as occurs in a high user throughput environment. The computers used were two Alienware intel i5 laptops with NVIDIA 1080 mobile GPUs and 16gb of RAM. The minimum specifications we would recommend would be and intel i5/ AMD R3 with a NVIDIA 1060 GPU in a desktop computer (which should be in a case that provides adequate airflow) with 8gb of ram. We support any VR compatible GPU that runs CUDA or OpenCL.Setup of software:NarupaXR is undergoing continuous development. Below we outline the process for loading a simulation into NarupaXR, however, we also note that we maintain online documentation (which we recommend using because they will be kept up to date as the code undergoes further improvements) at the following URLs: from links within . including the input files from NarupaXR from SteamVR should be downloaded from . A Steam account is required.Run the NarupaXR executable, and put on the VR headset. NarupaXR main menu with options will be displayed. To select an option the controller should be pointed at the menu in a similar fashion to pointing with a laser pointer.By pressing the Settings menu and then the Browse Server menu a VR server can be identified and connected to.The controller trigger (highlighted in yellow below), can be pressed whilst pointing at an atom to apply a force to the atom attracting it to towards the controller.While a controller is applying a force to an atom, the oscillating line indicates a force is being applied. This force is strongest when the controller is near an atom.The load simulation menu can be selected to change the molecule in the simulation.The load list contains the three simulations labeled as "docked" "undocked" and "QM chorismate"The DFTB+ server code is available at and should be built using the same procedure for OpenMM, decribed at . We are currently building a modified version of the fortran DFTB+ code, which we will make available in this repository after our modifications have been rebased onto the new GPL version of DFTB+.Verbal Introduction to students:In front of 1-5 students, the Instructor should hold out the headset and controllers. The instructor should first offer the opportunity for students to opt-out of using VR in the case of medical or personal reasons, this may include optouts for students with susceptibility to motion sickness.“Welcome to the VR lab, we are going to show you how in VR it is possible to interact with molecules that are running in simulations. We are going to conduct three experiments. First you are going to try and undock the chorismate molecule from chorismate mutase. The second experiment will be to see if you can rebind the chorismate into the active site. For the third experiment you are going to try and do the quantum rearrangement of chorismate into prephenate. In all of these experiments you will see an instructor in VR with you.”The instructor then holds up the headset:“This is the HTC Vive headset, it will track the motion of your head anywhere within the VR box that corresponds with the marking outlined on the floor. On the back of the headset there is a dial on it that will adjust how tight it is. You are welcome to wear eye glasses under the headset if you need too”The instructor then holds up the controllers:“These controllers will act as your “hands” in VR, if you point the end of your controller into a molecule and hold down the trigger on its underside then you will see a small line appear between the controller and the atom you have targeted. By continuing to hold down the controller trigger and moving your hand you will see that the atom will follow the controller’s position”The instructor should then ask the students to watch the monitor on the VR attached computer and perform the first undocking task with the following comment. “By pressing the controller trigger you can see how the molecule is responding to the position of the controller”Whilst still in VR the Instructor gestures towards the highlighted enzyme active site.“As you can see the active site has been highlighted separately from the rest of the enzyme and I’m able to reach in and grab chorismate”The Instructor should then pick a student and take them into VR to start the tasks.Procedure: Student puts the headset on and the unbound chorismate structure is loaded by the instructor.Instructor puts on their own headset and connect the same simulation server that the students is connected to using the procedure outlined above. Once connected the instructor should wave to student in VR and asks student to reach out and touch controllers (this confirms that headsets/controllers are in alignment and helps to familiarize the student with their new environment)Upon the student having unbound the substrate (determined by when the molecule is in free space) the instructor loads the second simulation. 5-minute time limit for student to work in this simulation.Upon the student finding a docked pose they are happy with the instructor loads the third simulation. 5-minute time limit for student to work in this simulation.The instructor asks the student to identify the vinyl group and perform the rearrangement. The students may need several attempts to perform the reaction, so the instructor should be ready to reset the simulation.Assessment:The questionnaire is loaded as part of the assessment module at the end of the lab. ................
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