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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hello all,<br>
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:<br>
<br>
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation <init><br>
INFO: running simulation: 100000 walkers, 1000 timesteps, p= 0.0<br>
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation <init><br>
INFO: dynamics duration 0.13<br>
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation initialiseWalkers<br>
INFO: writing initial walker positions<br>
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation initialiseWalkers<br>
INFO: walkr positions written<br>
0.0% <br>
<br>
However, if I use '-initial intra' I get the following:<br>
<br>
INFO: running simulation: 100000 walkers, 1000 timesteps, p= 0.0<br>
Jul 10, 2012 3:08:52 PM simulation.DiffusionSimulation <init><br>
INFO: dynamics duration 0.13<br>
<br>
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.
<br>
<br>
Many thanks,<br>
Damien<br>
<br>
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