Select group for least squares fit时选择中心分子组, Select group for output时选择System组。就是第...
Select group for centering时选择中心分子组, Select group for output时选择System组 2.gmx trjconv -s md.tpr -f cen.xtc -n index.ndx -o rot+trans.xtc -fit rot+trans 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...
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 ...
#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 ...
When prompted, select 4 (“backbone”) for both the least-squares fit and the group for RMSD calculation. The -tu flag will output the results in terms of ns, even though the trajectory was written in ps. The output plot shows the RMSD values relative to the initial structure in the mi...
atom: Atom name cgnr: Charge group number Charge groups define units of integer charge; they aid in speeding up calculations charge: Self-explanatory The qtot descriptor keeps a running count of the total charge on the molecule mass: Also self-explanatory typeB, chargeB, massB: Used for ...
GROMACS Tutorial GROMACS Introductory Tutorial Gromacs ver 3.3.1 Author: John E. Kerrigan, Ph.D. AST/IST, University of Medicine and Dentistry of NJ 675 Hoes Lane Piscataway, NJ 08554 Phone: (732) 235-4473 Fax: (732) 235-5252 Email: kerrigje@ 1 GROMACS Tutorial GROMACS Tutorial for Solva...
Select group for least squares fit时选择中心分子组, Select group for output时选择System组。就是第...