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gfrd / modern_egfrd

modern C++ implementation of eGfrd
GNU General Public License v2.0
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verbose mode #1

Open huytran216 opened 6 years ago

huytran216 commented 6 years ago

Hi, Thanks for the great tool and way less intimidating to install than previous version. It works!

Do you have a verbose mode, where the exact molecule position (in 3D) at east time step are written in the output file?

This is helpful for verifying e.g. FCS or FRAP measurements. Huy

Seynen commented 6 years ago

Hi Huy,

Thanks for the feedback. Glad to know that is works!

What do you mean with 'each time step'? The principle of GFRD does not know the positions of each particle at any given time (see description of the protective domains). Wat we can do is burst the domains at large time-intervals, and compute the particle positions. If small intervals are used, it would severely impact the computational benefits of the gfrd simulation principle.

I added a small feature that prints out the positions of the particles at a given interval. See simple.gfrd and class ParticlePositions in CopyNumber.hpp.

Let me know if it works for you.

Greetz, Marco

huytran216 commented 6 years ago

thank you.

A quick dumb question: Can we observe the correlation in the molecule position after each time interval? My hunch is both yes and no, depending on the molecules I want to monitor.

I will try to implement it Huy