Group 10 ( Prot-Masses) has 1960 elements Group 11 ( non-Protein) has 31932 elements Group 12 ( Water) has 31932 elements Group 13 ( SOL) has 31932 elements Group 14 ( non-Water) has 1960 elements Select a group: 13 Selected 13: 'SOL' Number of (3-atomic) solvent molecules: 10644...
Group 9 ( SideChain-H) has 484 elementsGroup 10 ( Prot-Masses) has 1960 elementsGroup 11 ( non-Protein) has 31932 elementsGroup 12 ( Water) has 31932 elementsGroup 13 ( SOL) has 31932 elementsGroup 14 ( non-Water) has 1960 elementsSelect a group: 13 参数文件内容: ; ions.mdp - us...
Will try to add 0 NA ions and 8 CL ions. Select a continuous group of solvent molecules Group 0 ( System) has 33892 elements Group 1 ( Protein) has 1960 elements Group 2 ( Protein-H) has 1001 elements Group 3 ( C-alpha) has 129 elements Group 4 ( Backbone) has 387 elements Group...
Selecta continuousgroupofsolvent molecules Group0(System) has33892elements Group1( Protein) has1960elements Group2( Protein-H) has1001elements Group3( C-alpha) has129elements Group4( Backbone) has387elements Group5( MainChain) has517elements Group6( MainChain+Cb) has634elements Group7( MainChain+H...
Select a group: 15 Selected 15: 'SOL' 用-pname和-nname指定的离子名称在以前的GROMACS版本中是特定于力场的,但在4.5版中已标准化。 指定的原子名称始终是所有大写字母中的元素符号,以及[moleculetype]。 残基名称可能会也可能不会附加charge符号(+/-)。 如果遇到困难,请参考ions.itp以获得适当的命名。
Group 2 ( SOL) has 6495 elements Select a group:--- Program: gmx trjconv, version ...
Group 12 ( Water) has 47811 elements Group 13 ( SOL) has 47811 elements Group 14 ( non-Water) has 3381 elements Select a group: 13 Selected 13: 'SOL' Number of (3-atomic) solvent molecules: 15937 Processing topology Back Off! I just backed up temp.topDDa7Ex to ./#temp.topDDa7Ex...
benzene.tpr -o rdf.xvg>需要经历选取group，如下Select a reference group and 1 groupGroup 0 (...
Group 1 ( Other) has 66 elements Select a group: 1 Selected 1: 'Other'Select a ...
根据提示,选择group 13 "SOL"作为嵌入的离子。千万别选成了蛋白质来替换离子。 在genion命令中,需要提供结构/状态文件(-s)作为输入文件,生成输出文件.gro (-o),处理拓扑文件(-p)反映替换掉的水分子和添加的离子,定义正负离子的名字(-pname和-nname),然后告诉genion添加中和体系电荷的正/负离子以及离子个数(-...