FSATOOL (short for "Fast Sampling and Analysis Tool") is a molecular dynamics simulation and trajectory data analysis program. It is developed by Chen, Changjun's group in Huazhong University of Science and Technology.
- Associate Prof. Chen, Changjun
- Meng, Fanjun (doctoral student, 2023-present)
- Gao, Junyong (graduate student, 2022-present)
- Wu, Mincong (doctoral student, 2021-present)
- Liao, Jun (doctoral student, 2020-present)
- Shu, Zirui (graduate student, 2020-2023)
- Zhang, Haozhe (graduate student, 2018-2021)
- Gong, Qiankun (graduate student, 2017-2020)
- Zhang, Haomiao (doctoral student, 2016-2021)
- Molecular dynamics simulation in implicit and explicit solvent (GB, PME, GPU acceleration) (Ref.2, Ref.3)
- Collective variable calculation for MD trajectory (Ref.2)
- Enhanced sampling in collective variable space and temperature space (SMD, REMD, ABMD) (Ref.1, Ref.2, Ref.3)
- Dimensionality reduction and free energy calculation (PCA, TICA, SRV, TAE; GMM, WHAM, MBAR) (Ref.1, Ref.2, Ref.3)
- Markov state model analysis and transition path calculation (Ref.1)
- Electrostatic potential, solvation free energy and binding free energy calculation (MM-PBSA/GBSA, GPU acceleration) (Ref.4)
- Massive molecular structure clustering (one million) (K-medoids, GPU acceleration) (Ref.5)
FSATOOL reference manual is on the web page.
- Download and Install NVIDIA HPC SDK (NVHPC, version 22.5) (https://developer.nvidia.com/nvidia-hpc-sdk-downloads).
- Set up the NVHPC environment by the module file in the directory ${NVHPC_HOME}/modulefiles/nvhpc/ and ensure NVHPC's compilers (nvcc, nvfortran, mpicc, mpif90) are working properly.
- Download the FSATOOL repository by "git clone /~https://github.com/fsatool/fsatool.github.io".
- Unzip the latest FSATOOL source code package in the cloned FSATOOL repository and change path into the unzipped directory.
- Run 'make preparelib' to install NETCDF and FFTW libraries.
- Run 'make' to compile FSATOOL source codes
- Copy the generated executable file "fsatool" to any place you want to do the simulation or analysis work.
Execute the command "mpirun -n nproc fsatool modname taskname -i inputfile"
"nproc" is the number of processes in the calculation.
"modname" specifies the module to run.
"taskname"(optional) gives the task name in each module.
"inputfile"(optional) is a user-defined input parameter file.
All the available modname, taskname and default input files are listed as follows:
modname=sim, inputfile=sim.in
modname=msm, inputfile=msm.in
taskname=cluster inputfile=cluster.in
taskname=lumping inputfile=lumping.in
taskname=tpt inputfile=tpt.in
taskname=check inputfile=check.in
taskname=tram inputfile=tram.in
taskname=picksnap inputfile=picksnap.in
modname=analysis, taskname=wham, inputfile=wham.in
taskname=gmm, inputfile=gmm.in
taskname=freehis, inputfile=freehis.in
taskname=contactmap, inputfile=contactmap.in
taskname=phi, inputfile=phi.in
taskname=anm, inputfile=anm.in
taskname=cv, inputfile=cv.in
taskname=reducedim, inputfile=reducedim.in
taskname=deep, inputfile=deep.in
modname=normalmode, taskname=anm inputfile=anm.in
taskname=qha inputfile=qha.in
taskname=nma inputfile=nma.in
modname=surfpb, inputfile=surfpb.in
[1] Haomiao Zhang, Qiankun Gong, Haozhe Zhang, and Changjun Chen
FSATOOL: A useful tool to do the conformational sampling and trajectory analysis work for biomolecules.
J. Comput. Chem. 2020, 41, 156-164
[2] Zirui Shu, Mincong Wu, Jun Liao and Changjun Chen
FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program.
J. Comput. Chem. 2022. 43: 215-224
[3] Mincong Wu, Jun Liao, Zirui Shu and Changjun Chen
Enhanced sampling in explicit solvent by deep learning module in FSATOOL.
J. Comput. Chem., 2023. 44: 1845-1856.
[4] Jun Liao, Zirui Shu, Junyong Gao, Mincong Wu and Changjun Chen
SurfPB: A GPU-accelerated electrostatic calculation and visualization tool for biomolecules.
J. Chem. Inf. Model, 2023. 63: 4490-4496.
[5] Junyong Gao, Mincong Wu, Jun Liao, Fanjun Meng, Changjun Chen
Clustering one million molecular structures on GPU within seconds.
J. Comput. Chem. 2024, https://onlinelibrary.wiley.com/doi/10.1002/jcc.27470
We gratefully acknowledge the support from the National Natural Science Foundation of China (NSFC).
If you have any question, please contact Chen, Changjun
- Email: cjchen@hust.edu.cn