MOLDY CEC Inha University ChiOk Hwang MOLDY General

MOLDY CEC Inha University Chi-Ok Hwang

MOLDY • General molecular dynamics (MD) package • GNU general public license • highly portable • parallelized • Only pairwise central force models and point-charge electrostatics • Newton-Euler equations of rotational dynamics

Handling Long-ranged Forces: Ewald Sum • Technique for efficiently summing the interaction between an ion and all its periodic images • Each point charge surrounded by a charge distribution of equal magnitude opposite sign with a Gaussian distribution • Cancelling distribution; charge distribution of the same sign as the original charge and the same shape

Handling Long-ranged Forces: Ewald Sum • Cancelling distribution summed in reciprocal space • Final potential energy = real space sum + reciprocal space sum – (self_term + surface term)

MOLDY input

MOLDY input

MOLDY input: Example

MOLDY input

MOLDY input

MOLDY input: Example

MOLDY input

MOLDY input

MOLDY input: Example

MOLDY output

Parallelization • “Replicated data” approach - each processor maintaining a complete set of dynamical variable arrays for all particles; shortranged and reciprocal-space force calculations are divided among the processors - simplicity of programming - straightforward load-balancing - coarse communication granularity - efficient for small and medium-sized systems - poor scaling to very large numbers of processors