Molecular Mesh Generation

 

Mesh generation for molecular systems (including surface triangular mesh and volume tetrahedral mesh) emergs an urgent issue in some mathematical modelings and numerical simulations (such as boundary element/finite element computation) of realistic biomolecular systems. Most tranditional tools were designed for molecular visualization and structural geometric analysis, but they are not robust enough, or the generated meshed are not qualified enough for numerical simulations.

 

We recently developed a robust method for meshing molecular Gaussian surface: TMSmesh -- A robust method for molecular surface mesh generation using a trace technique. And the improved version guarantees a (triangulated) manifold mesh.

 

TMSmesh download and notation:
The binary versions of TMSmesh (under Linuxi86_64) are released and can be downloaded here:

The first version of TMSmesh (click TMSmesh to download), the algorithm was described in [1]

The second version of TMSmesh (click TMSmesh_2012_11 to download), the algorithm was described in [2]

(This version guarantee the generated mesh is a (trangulated) manifold mesh, but the speed is currently several times slower than the old version.)

A quick guide for usage of the second version:

command line style:

cd TMSmesh

./TMSmesh xxx.pqr h d c

(Notice: the pqr file should be put in the folder named "pqr". The output .off file is in the folder named "off". )

Example: ./TMSmesh adp.pqr 1.0 0.5 1.0

h relates to the mesh density. when h reduce,the grid density increase.
d is a parameter called decay rate in the Gaussian surface.
c is a parameter called isovalue in the Gaussian surface and controls the volume enclosed by the Gaussian surface.

In addition, a PQR benchmark set of molecular/macromolecular structures for meshing test is also prepared and downloadable.

 

TMSmesh shows its potential capability to handle arbitrary size of molecular systems available in PDB. Furthermore, the generated mesh can be directly used in boundary element simulation of Poisson-Boltzmann electrostatics such as using software AFMPB.

 

Journal references:

[1] Minxin Chen, Benzhuo Lu, J. Chem. Theory Comput., 7:203-212, 2011

[2] Minxin Chen, Bin Tu, Benzhuo Lu, Triangulated Manifold Meshing Method Preserving Molecular Surface Topology, Journal of Molecular Graphics and Modelling, 38: 411-418, 2012

 

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本页面的中文版 (In Chinese)

 

分子网格产生

 

分子表面网格产生程序 TMSmesh (Linuxi86_64,可执行版本),

点击下载第一个版本(TMSmesh), 算法见【1】

点击下载第二个版本(TMSmesh_2012_10), 算法见【2】

(这个版本保证产生的网格为manifold mesh,但它的计算速度比老版本慢了若干倍)

另外,这里也可下载一个从小分子到大分子结构的 PQR测试集 PQR benchmark.

TMSmesh 是为生成任意大小分子体系的高质量表面网格而设计的,它已在超过一百万个原子的病毒分子上测试成功。而且,TMSmesh 产生的分子表面网格也经测试可直接用于边界元方法的计算模拟中,如用软件 AFMPB 求解PB静电。

 

参考文献:

[1] Minxin Chen, Benzhuo Lu, J. Chem. Theory Comput., 7:203-212, 2011

[2] Minxin Chen, Bin Tub, Benzhuo Lu, Triangulated Manifold Meshing Method Preserving Molecular Surface Topology, Journal of Molecular Graphics and Modelling, 38: 411-418, 2012

作者:Minxin Chen陈旻昕),Tu Bin (涂斌)Benzhuo Lu卢本卓)。