最终选中心分子为COO, SDF的原子为体系中所有的水使中心分子在盒子内居中, 同时所有其他分子处于盒子内 gmx_mpi trjconv -s md0.tpr -f md0.trr -n sdf.ndx -o md0_cnt.xtc -center -ur compact -pbc molSelect group for centering时选择中心分子组, Select group for output时选择System组按中心分子对...
Select group for centering Group 0 ( System) has 33876 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 5 ( MainChain) has 517 elements Group 6 ( MainChain+Cb) has 6...
Select group for centering时选择中心分子组,Select group for output时选择System组 按中心分子对轨迹进行叠合, 移除中心分子的转动和平动 gmx_mpi trjconv -s md0.tpr -f md0_cnt.xtc -n sdf.ndx -o md0_cnt_fit.xtc -fit rot+trans Select group for least squares fit时选择中心分子组,Select group ...
Select group for least squares fit时选择中心分子组, Select group for output时选择System组 gmx spatial -s md.tpr -f rot+trans.xtc -n index.ndx -nab 300 Select group to generate SDF时选择要统计SDF的组, Select group to output coords (e.g. solute)时选择中心分子组 2作图 将gOpenMol解压后,...
Select group for least squares fit时选择中心分子组, Select group for output时选择System组 gmx spatial -s md.tpr -f rot+trans.xtc -n index.ndx -nab 300 Select group to generate SDF时选择要统计SDF的组, Select group to output coords (e.g. solute)时选择中心分子组 ...
Select group for output
Group 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 - used as input into grompp to generate ions.tpr; Parameters describing what to do, when to stop and what to saveintegrator = ...
Select group for centering时选择中心分子组, Select group for output时选择System组 第三步：按中心...
SelecttheForceField: From'/public/software/.local/easybuild/software/GROMACS/2021-gromacs-cpu-new/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem.24,1999-2012,2003) 2: AMBER94forcefield(Cornell et al., JACS117,5179-5197,1995) ...
#Select 1 ("Protein") as the group to be centered and 0 ("System") for output 1. 2. RMSD计算 gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns #计算模拟后的 #Choose 4 ("Backbone") for both the least-squares fit and the group for RMSD calculation ...