ndx -dens num -d z -sl *** 统计的是某一帧的选定的某离子的数密度的话，输入gmx density -f...
1.1. 创建拓扑与坐标文件 gmxeditconf- 编辑模拟盒子以及写入子组(subgroups) gmxprotonate- 结构质子化 gmxx2top- 根据坐标生成原始拓扑文件 gmxsolvate - 体系溶剂化 gmxinsert-molecules- 将分子插入已有空位 gmxgenconf- 增加”随机”取向的构象 gmxgenion - 在能量有利位置加入单原子离子 gmxgenrestr- 生成索引...
were built up and optimized fully at the B3LYP/6–31+G(d,p) level within the density ...
gmx densmap computes 2D number-density maps. It can make planar and axial-radial density maps. The output .xpm file can be visualized with for instance xv and can be converted to postscript with xpm2ps. Optionally, output can be in text form to a .dat file with -od, instead of the ...
The GMX GRANUMEIST®High Shear Granulator and Mixer is designed for efficient and homogenous wet granulation of powders to form a medium to high density granule. Its top-drive design allows for easy cleaning and maintenance, faster processing times, and superior user safety. ...
number_density: Use the first two factors. This produces a number density as a function of distance. none: Use only the first factor. In this case, the RDF is only scaled with the bin width to make the integral of the curve represent the number of pairs within a range. Note that excl...
gmx densmap computes 2D number-density maps. It can make planar and axial-radial density maps. The output .xpm file can be visualized with for instance xv and can be converted to postscript with xpm2ps. Optionally, output can be in text form to a .dat file with -od, instead of the ...
然后利用指令:g_energy -f npt.edr -b 40 -e 100 -o density2.xvg,屏幕中自动会帮你计算平均值,比如密度是986.168 g/L。最后利用指令:editconf -f npt.gro -density 986.168 -o npt2.gro调整密度。npt2.gro就成了最终的构型。 24、0; 图1 npt系综密度对时间的关系 问题2:遇到一个极其恼人的...
8: The dielectric interface is implemented analytically with the revised density function approach (sasopt = 2). The linear equations on the irregular points are constructed using the secondorder harmonic average method. inp (Default = 2) 计算非极性溶剂自由能的方法1: The total non-polar ...
先利用指令:g_energy-fnpt.edr-odensity.xvg了解密度的波动,然后选择合适的计算范围。比如CO2在H2O的npt后得到密度波动见图1,我们发现40ps后密度相对比较稳定,于是从40ps到100ps做个平均值。 然后利用指令:g_energy-fnpt.edr-b 40 -e 100 -o density2.xvg,屏幕中自动会帮你计算平均值,比如密度是986.168 g/...