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 ...
part_mol_com, 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 histogrammi...
若是没有明智地提前将原子名称区分好,或是即使用Select语法也无法选定特定的组,就只好通过建立相应的索引文件了。在distance与gangle等命令中所用的组往往需要选定两个位置,这两个位置应当在索引文件中成对出现。若是作为向量,则是从第一个向量指向第二个向量。同理,对于需要三个位置的组,则应三个为一行。下面是...
all frames all written to one file..pdbfiles with all frames concatenated can be viewed withrasmol-nmrpdb. It is possible to select part of your trajectory and write it out to a new trajectory file in order to save disk space, e.g. for leaving out the water from a trajectory of a ...
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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)...
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...