search

yunhuige / toy_binding

GitHub for the toy_binding project
0 stars 0 forks source link

mismatch between COM distances files generated from pulling simulation and my own calculations #3

Closed yunhuige closed 6 years ago

yunhuige commented 6 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 6 years ago

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