TAPS released in 2024 (Travelling-salesman based Automatic Path-Searching)

Requirements

• GROMACS >=2019.4
• Plumed >=2.7
• Cuda >=10.2
• Openmpi >=4.0.2
• python >=3.7.4
• numpy >=1.17.2
• MDTraj >=1.9.3
• GromacsWrapper >=0.8.0
• mpi4py >=3.0.3
• concorde :
• These requirements were tested and proved to work. Feel free to test

Install Python and Python Packages

We highly recommend that you download the Python 3.x version of Anaconda, which is a completely free enterprise-ready Python distribution for large-scale data processing, predictive analytics, and scientific computing.

Design and Usage

Travelling-salesman based Automatic Path-Searching (TAPS)

• No static coordinate space (CVs): ordered high dimensional conformations
• Perpendicular relaxation: Quickly find MFEP segments
• Automatic re-order of path nodes by Travelling-salesman
• Enhanced sampling along path on PCV-z by MetaD
• Validated for three protein systems (76-303 residues and total 30000-80000 atoms, TAPStest)

Tutorial

1. The parameters used for TAPS can be modified in pars/taps.par file
2. Serial Running:

     1. Change runMode to "serial" in taps.par
     2. > python runTAPS.py                                  

3. Parallel Running:

     1. Change runMode to "Parallel" in taps.par
     2. > mpirun -np 8 python runTAPS.py          

TODO

[ ] Update Tutorial

[ ] Test more

Authors:

Lizhe Zhu: zhulizhe@cuhk.edu.cn

Song Liu: sliubu@connect.ust.hk

Kun Xi: xikun@cuhk.edu.cn

Contributors:

Maybe you !