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Simulations
of the Tomato Bushy Stunt Virus Capsid

### Abstract:

*The spherical protein capsid of the tomato bushy stunt virus expands
by 10%when calcium ions are removed from the system and the pH is
raised above 7[50]. We have attempted to simulate
this effect using molecular dynamics. Although we calculate
velocities for only the three proteins of the asymmetric unit plus
associated ions, we include the nonbonded interactions of all 180
proteins (nearly 500,000 atoms) in the virus coat. The Cell-Multipole
Method (CMM)[51] enables us to calculate the nonbond
interactions in this gigantic system. Also, in order to increase the
timelength of the simulation, we employ internal coordinate dynamics,
using Newton-Euler Inverse Mass Operator (NEIMO)
Dynamics[53], which enable us to use timesteps of 2
femtoseconds for proteins of this size.
*

*ktl@sgi1.wag.caltech.edu *

Sat Jun 18 14:06:11 PDT 1994