Maximum Flux Transition Paths of Conformational Change
with the Post Lab
Project description
Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B.
Such a calculation is more informative and more manageable if done for a reduced set of collective variables chosen so that paths cluster in collective variable space.
The maximum flux transition path (MFTP) is defined as a path that crosses each isocommittor at a point which (locally) has the highest crossing rate of distinct reactive trajectories.
Such a path is nearer to an ideal path than others that have been proposed with the possible exception of the finite-temperature string method path.
In particular, the MFTP is a finite-temperature correction to the minimum free energy path (MFEP).
Simplified Maximum Flux Transition Path
- Example 1: Simple example using MFTP [1] where collective variables are configurations.
- Click here to download.
- After unpacking, review README.txt for a description of contents and usage instructions.
- Example 2: Alanine dipeptide in a vacuum (CHARMM)
- Click here to download.
- After unpacking, review README.txt for a description of contents and usage instructions.
- Example 3: Alanine dipeptide in a vacuum (NAMD)
- Click here to download.
- After unpacking, review README.txt for a description of contents and usage instructions.
Maximum Flux Transition Path
- Example 1: Alanine dipeptide in a vacuum (CHARMM)
- Click here to download.
- After unpacking, review README.txt for a description of contents and usage instructions.
Minimum Free Energy Path
- Example 1: Simple example using MFEP [1] where collective variables are configurations.
- Click here to download.
- After unpacking, review README.txt for a description of contents and usage instructions.
References:
[1] R. Zhao, J. Shen, and R.D. Skeel,
"Maximum flux transition paths of conformational change,"
J. Chem. Theory Comput. 6, 2010, 2411-2423.