[Camino-users] ply files in Monte Carlo simulations

[Damien McHugh]

Hello all,
I am having trouble running simulations of intra-cellular diffusion when using .ply files as substrates. If I set '-initial extra' the simulation will run, with the terminal output showing, for example:

Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation <init>
INFO: running simulation: 100000 walkers, 1000 timesteps, p= 0.0
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation <init>
INFO: dynamics duration 0.13
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation initialiseWalkers
INFO: writing initial walker positions
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation initialiseWalkers
INFO: walkr positions written
0.0%

However, if I use '-initial intra' I get the following:

INFO: running simulation: 100000 walkers, 1000 timesteps, p= 0.0
Jul 10, 2012 3:08:52 PM simulation.DiffusionSimulation <init>
INFO: dynamics duration 0.13

The simulation does not progress from here and 0.0% doesn't print to the terminal. Any advice regarding the use of ply files is much appreciated.

Many thanks,
Damien

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