“overlap_matrix.svg” 包含了一个重叠矩阵图,良好的重叠要求第一条上下对角线至少为0.03,不同的λ方案可以帮助改善重叠。 参考资料:1. Carvalho Martins, L., Cino, E. A. & Ferreira, R. S. PyAutoFEP: An automated free energy perturbation workflow for GROMACS integrating enhanced sampling methods. ...
1）自由能微扰（Free Energy Perturbation，FEP）和热力学积分（Thermodynamic Integration，TI）方法 FEP的...
本例中输入以下命令来生成星状微扰图谱,以“FXR_12”作为中心分子,指定输入的配体分子为“lig_data”文件夹中的分子。 generate_perturbation_map.py --map_type=star --map_bias=FXR_12 --input lig_data/*.mol在工作目录可打开“est_graph.svg”文件查看生成的图谱。 04准备输入参数文件 下面我们需要使用“...
Subsequently, thermodynamic integration or free energy perturbation methods can be applied to calculate the difference in binding free energy between two states, such as ligand-bound and ligand-free protein. These methods involve calculating the potential energy differences between the states and integratin...
24、up numbercharge groups define units of integer charge; they aid in speeding up calculations charge: self-explanatorythe qtot descriptor keeps a running count of the total charge on the molecule mass: also self-explanatory typeb, chargeb, massb: used for free energy perturbation (not discus...
energygrps = group#1 group#2 ... SOL nstlist = 10 ;for Neighbor Searching:nstlist = (10)[steps]ns_type = grid/simple ;the fomer is faster than later for large system! pbc = xyz/no ; use or no periodic boundary conditions.rlist = (1)[nm]
Self-explanatory The "qtot" descriptor keeps a running count of the total charge on the molecule mass: Also self-explanatory typeB, chargeB, massB: Used for free energy perturbation (not discussed here) Subsequent sections include [ bonds ], [ pairs ], [ angles ], and [ dihedrals ]. ...
一个使用gromacs进行蛋白质模拟的入门教程 GROMACS Tutorial Lysozyme in Water Justin Lemkul Department of Biochemistry, Virginia Tech This example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step ...
with mass and constraints free-energy perturbation, domain @@ -1413,7 +1413,7 @@ problem for long production MD, but you might prefer to do some kinds of work, e.g. that runs very few steps, on just the CPU (e.g. see ``-nb`` above). The same ``-gpu_id`` option (or ``...
? typeB, chargeB, massB : Used for free energy perturbation (not discussed here) Subsequent sections includ e [ bonds ], [ pairs ], [ angles ], and [ dihedrals ]. Some of these sections are self-explanatory (bonds, angles, and dihedrals). The parameters and function types associat...