Scientific Computing

• FEniCs (FEniCs source code, Demos): open-source computing platform for PDEs.

• LINPACK: Collection of Fortran subroutines that analyze and solve linear equations and linear least-squares problems.

• MUMPS: A parallel sparse direct solver.

• NumPy:  Fundamental package for scientific computing with Python.

• PARDISO: Software for solving large sparse symmetric and unsymmetric linear systems of equations.

• PETSc: A software library for parallel solution of PDEs.

• Python: Apowerful programming lagrange.

• SciPy: Python-based ecosystem of open-source software for mathematics, science, and engineering.

• SUITESPARSE: A Suite of sparse matrix software.

• WSMP: Collection of algorithms for efficiently solving large sparse systems of linear equations.

• Bempp-cl: Open-source boundary element method library 

Computational Molecular Biology

• CHARMM: Chemistry at HARvard Macromolecular Mechanics.

• DelPhi: Provides numerical solutions to the Poisson-Boltzmann equation.

• OpenMM (Omina): It is CPU / GPU accelerated molecular dynamics with an intuitive Python interface.  Wrappers for C, C++, and Fortran.

• PDB: Protein Data Bank.

• PDB2PQR: Convert PDB files into PQR files.

• VMD: Molecular visualization program.

• CHARMM-GUI: 

Molecular Surface and Volume Mesh Generation Package.

• MSMS:  SES, install instruction by anaconda

• NanoShaper: Surface Type - SES, Skin,  Blobby, Gaussian Surface 

• TMSmesh: Gaussian Surface 

• GAMer: Geometry-preserving Adaptive Mesher

• Molecular Graphics Software

Ion Channel Package

• CHAP: A new tool for the functional annotation of novel ion channel structures

• CIMS: Courant Institute of Mathematical Sciences -- New York University, USA

• IMA:  Institute for Mathematics and its Applications -- University of Minnesota, USA

• Fields: The Fields Institute for Research in Mathematical Sciences -- Toronto, Canada

• ICERM: Institute for Computational and Experimental Research in Mathematics -- Providence, USA

Numerical Linear Algebra

• Michele Benzi (Emory University, USA)

•  Nick Higham (University of Manchester,UK)

• Yousef Saad (University of Minnesota, USA)

• Michael Saunders (Stanford University)

• Valeria Simoncini (Universita' di Bologna,Italy)

• Daniel B. Szyld (Temple University, USA)

• Andrew Wathen (University of Oxford, UK)

• Jianlin Xia (Purdue University, USA)

• David Watkins (Washington State University, USA)

Computational Biology and Chemistry

•  Tamar Schlick (Courant Institute of Mathematical Sciences, New York University, USA)

• L. Ridgway Scott (University of Chicago, USA)

Ion Channel Simulations

• Benoit Roux (University of Chicago)

• Shin-Ho Chung (Australian National University)

• Ben Corry (Australian National University) 

• Robert Eisenberg (Rush Medical College) 

• Michael Grade (University of California-San Francisco)

• Maria Kurnikova (Carnegie Mellon University)

• Tzyy-Leng Horng (Feng Chia University, Taiwan)

• Jinn-Liang Liu (National Tsing Hua University, Taiwan)

• Weishi Liu (University of Kansas)

• Benzhuo Lu (Chinese Academy of Sciences)

• Dexuan Xie (University of Wisconsin-Milwaukee) 

• Carl Garder (Arizona State University)

Boundary Element Method

• Timo Betcke (University College London) 

Life

• For potential Ph.D. students

Study

• PDB文件格式说明(Chinese)

• APBS教程

• 分子模拟论坛

Latex

Others

•  N and NP problems introduction (Chinese version)