Michal Koutek, Jeroen van Hees, Frits H. Post, AF Bakker

Talk overview 

• Introduction to Molecular Dynamics (MD) 

• Motivation for particle steering 

• MolDRIVE system & MD simulations 

• 3D interaction & visual force feedback 

– spring tools can compete with haptics 

• Particle steering methods 

– virtual particle 

– virtual particle with spring manipulator 

– visual spring force feedback 

• Video presentation of particle steering tools 

• Conclusions & future work 

Virtual Spring Manipulators for Particle Steering in MD Simulations 

Michal Koutek, Jeroen van Hees, Frits H. Post, A.F. Bakker

MolDRIVE Application Overview 



Introduction to Molecular Dynamics Simulations 

• MD simulation: numeric solutions of Newton’s equations 

– Goal: better insight in material properties and 

behavior of complex particle systems 

– How: discrete simulation timesteps of ± 10-15 s 

• Just for an idea of atomic size: 



Introduction to Molecular Dynamics Simulations 

• Newton’s equations of motion 

∂ p i 

∂t 

∂U 

( r) 

= Fi 

= − 

∂ri 

∂ri 

∂t 

p i = 

m 

( Force is calculated from potential…) 

i 



MD Simulation Programs 

MD simulation runs in parallel on supercomputers. 

• We have used: 

– DEMMPSI, GROMAX 

• Other existing: 

– NAMD, AMBER, etc. 



Motivation for particle steering in MD 

Particle (atomic) steering: 

- manipulation of particles in MD simulation by the user 

Goals: - overcome energy barriers in simulated particle system 

- interactively experiment with simulation 

How: - directly reposition particles to another location 

- adding external force on particles 

( and observe what happens … ) 

Applications: 

- protein design, molecular docking 

- body / anti-body simulations, medicine, chemistry, etc... 

The MD community has a great interest for atomic steering… 



VR for Molecular Dynamics 

• VR offers: 

– 3D immersion 

into the microscopic scale virtual models 

– 3D interaction devices give the opportunity 

to interact with simulations and particles 

=> virtual laboratory for MD experiments 



VR and Molecular Dynamics 









MolDRIVE System 

• VR system for visualization and steering 

of real-time remotely running MD simulations 

• interface to several MD simulation programs 

(DEMMPSI, GROMAX) 

• MD simulations run on remote supercomputers 

(CRAY T3E - 128 proc., SGI 1100/1200 Beowulf Linux Cluster -54 proc., 

SGI Origin 2000 - 8 proc.) 

• VR visualization & steering from the Responsive Workbench 

(runs on SGI Onyx 2 - 4 processors, Infinite Reality graphics) 

• (MolDRIVE and DEMMPSI developed at TU Delft..) 



MolDRIVE Architecture 

Simulation clients: 

• implemented in C++ using MPI 

• domain decomposition of space 

Visualization client: 

• implemented in C++ using RWB 

Library, Open GL & Performer 



MolDRIVE Interaction & Visualization Tools 

• RWB Library: 

– basic interaction function (object selection & manipulation - 

direct or ray-casting) 

– basic set of 3D widgets 

• MolDRIVE: 

– MD specific particle selection techniques 

– simulation control with instant replay (video controller metaphor) 

– particle visualization & legend 

– visualization of derived volumetric particle (particle densities, 

kinetic and potential energy, force fields, etc. ) 

– real-time visualization techniques: 

• color slicers, landscape slicers, vector slicers (Plexi-Pad - defines a 

cutting plane through the data) 

• iso-surfaces, point-based volume rendering 



MolDRIVE Interaction & Visualization Tools 



MolDRIVE - Particle Steering Methods 

• virtual particle steering method 

• virtual particle with spring manipulator 

• visual spring force feedback method 

We need a force input tool: 

- haptics devices ? 

- visual force feedback using spring tools ? 



Force Feedback in VR 

Haptic force feedback 

[Haptic Workbench] 

[Phantom & MD] 

Visual force feedback 

- using spring tools 

[Spring Manipulator] 



MolDRIVE - Particle Steering Methods 

1) virtual particle 

steering method 

2) virtual particle 

with spring manipulator 

3) visual spring force 

feedback method 



Virtual Particle Method 

• virtual particle (blue) - desired position is sent as feedback to the simulation; 

(If the new position is accepted then the particle moves there..) 

•white particle - accepted position 




Particle acceptance rule: 




[Beta-Alumina electrolyte simulation] 




Disadvantage: 

• virtual particle always follows user’s motion, while 

the accepted particle only moves when simulation 

allows it… 

=> inconsistent view ! 

Solution: 

• using the Spring Manipulator, which always stays 

connected with the original particle.. 



Virtual Particle with Spring Manipulator 




Virtual Particle with Spring Manipulator 

Spring Manipulator: 

• 2 DOF (stretching,bending) 

Spring Manipulator is based 

on the Spring-fork .. 



Spring manipulation tools: 

… presented at EG VE 2001 ... 

• spring 

- attached to the object center, linear motions 

- tool has 1 DOF - the length of the spring 

- and controls 3 DOF - xyz of the object 

• spring-fork 

- attached to the object, defines a contact point for transfer of forces 

- both translations and rotations 

- tool has 3 DOF - extension, bend, torsion of the spring 

- and controls 6 DOF - xyz + hpr of the object 

• spring-probe 

- used for probing the material stiffness or pushing to an object 

- tool has 1 DOF - the length of the spring 

- and controls 3 DOF - xyz of the object or 1 DOF - pressure 



Spring-fork in Action 

• spring-fork 

- attached to the object, defines a contact point for transfer of forces 

- both translations and rotations 

- tool has 3 DOF - extension, bend, torsion of the spring 

- and controls 6 DOF - xyz + hpr of the object 



Spring Manipulator Deformation Model 

Spring Manipulator: 

• 2 DOF (stretching,bending) 



Spring Manipulator with Force Feedback 



Spring Manipulator with Force Feedback 



Visual Spring Force Feedback Steering Method 





Particle selection: 

Spring constant controls the strength 

of the Spring Manipulator... 










[Carbon polymer simulation] 



MolDRIVE Video 

Let’s see the video... 



Conclusions 

• Virtual particle steering methods 

– useful for navigation of particle through low energy 

barriers with little disturbance of simulation 

– spring manipulator gives a nice feedback when the user 

tries to place a particle (atom) on given position rather 

then push it to that location which does the spring force 

manipulator 

• Spring force feedback steering 

– the smoothest way of steering the MD simulation 

to a desired state 

– intuitive and makes sense of underlying physics 

– visual experience of the inter-atomic forces 



Conclusions 

• MolDRIVE 

– “wonderful VR MD laboratory” 

– amazing experiments on nanoscopic scale 

– applications from chemistry, medicine, material science 

Future work: 

– to be able to manipulate atomic groups 

and whole molecules 



Time for questions 

Any questions, please? 

More about MolDRIVE and particle steering: 

http://visualization.tudelft.nl/~michal

Michal Koutek, Jeroen van Hees, Frits H. Post, AF Bakker

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