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yunhuige / toy_binding

GitHub for the toy_binding project
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mismatch between COM distances files generated from pulling simulation and my own calculations #3

Closed yunhuige closed 5 years ago

yunhuige commented 5 years ago

This is not an issue of unbiased simulation. But it is very important to dTRAM/TRAM calculation. I double checked COM distances files generated from pulling simulation and I found it is different from my own calculations. If that's the case then everything in the current dTRAM/TRAM calculation is wrong! I'm not sure if GROMACS consider pbc treatment in calculating these distances. I thought it should but now I'm confused. Need work on this later.

yunhuige commented 5 years ago

It's confirmed that output distances from GROMACS are CORRECT!