gmx select结合-oi和gromacs的selection选择语句(看手册)原理上可以实现,但我肯定自己写VMD tcl脚本,...
例如在一条碳链中,每个碳最好分别命名为"C1""C2"...而不能统一命名为"C",这样将很难通过Select语法来甄别。例如,要是要计算一条碳链与z轴之间的夹角,则可以使用命令gmx gangle -f ..xtc -s ..tpr -n ..ndx -g1 vector -group1 'name C1 C5 permute 1 2' -g2 z -oav -oall -oh。此处的...
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...
我想用gmx select 在index里建立一个group 这个group包括Z>80的所有水分子 我输入gmx select -s md....
selectsel_peptide, chain X 然后抽取多肽链保存到另一个对象 extractpeptide, sel_peptide 计算并显示蛋白的溶剂可及表面 assurface, 1klu 对蛋白表面和多肽使用两种可区分的颜色进行着色 colorwhite, 1klu colortv_blue, peptide 选择处于多肽5埃之内的所有蛋白残基进行着色, 这构成了蛋白-多肽的界面 ...
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Option -sep can be used to write every frame to a separate .gro, .g96 or .pdb file. By default, all frames all written to one file. .pdb files with all frames concatenated can be viewed with rasmol -nmrpdb. It is possible to select part of your trajectory and write it out to ...
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