part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog -select <selection> Position pairs to calculate distances for -len <real> (0.1) Mean distance for histogramming -tol <real> (1) Width of full distribution as fraction of -len -binw <real> (0.001) Bin width for ...
xtc -tu ps -select 'resid 8060 and name SD plus resid 8007 and name N6' -oall distance....
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...
楼主可以试试这个命令：gmx distance -f *.xtc -s *.tpr -select 'com of group *A plus com ...
box大小是9.15084 9.15084 12，我用gmx select -f md.gro -on →rdist = distance from ...
use-xy. To set the bin width and maximum distance to use in the RDF, use-binand-rmax, respectively. The latter can be used to limit the computational cost if the RDF is not of interest up to the default (half of the box size with PBC, three times the box size without PBC). To...
The RMSD at time t is calculated as the RMS of the differences in distance between atom-pairs in the reference structure and the structure at time t. gmx rmsdist can also produce matrices of the rms distances , rms distances scaled with the mean distance and the mean distances and matrices...
When eneopt = 1, this is the cutoff distance used for van der Waals interactions only. The particle-particle portion of the Coulombic interactions is computed with the cutoff of cutfd. nsnba (Default = 1)Sets how often (steps) atom-based pairlist is generated. decompopt (Default = 2)...
options->addOption(SelectionOption("select") .storeVector(&sel).required().multiValue() .deion("Groups to calculate distances to")); options->addOption(DoubleOption("cutoff").store(&cutoff) .deion("Cutoff for distance calculation (0 = no cutoff)")); ...
res and atom of -pbc. All three options give different results for triclinic boxes and identical results for rectangular boxes. rect is the ordinary brick shape. tric is the triclinic unit cell. compact puts all atoms at the closest distance from the center of the box. This can be useful ...