Dear Amber,
I want to generate a series of configurations as the starting input files for the umbrella sampling windows along a reaction coordinate from a equilibrium trajectory file(.nc) by a QM/MM simulation,I have a few questions about how to extract the snapshop from the trajectory file , for example, atom A and B will be break and the distance between them are 6.0 angstrom，atom C and D will generate a new covalent bond and the distance between them are 4.0 angstrom,
How to select the length of the reaction coordinate (6.0 or 4.0)?
How to determine the space (0.2 angstrom?) between the adjacent frames and how many windows (20 frames for 4.0 reaction coordinate)(.rst) should be extract from the trajectory file?
Are there any available tutorial for umbrella sample by QM/MM using Amber?
It is highly appreciate for any suggestion.
Zhihong Xin
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Received on Sun Mar 14 2021 - 03:30:02 PDT
