gmx

HIS/HID/HIP

科学网—#笔记#氨基酸残基质子化形式的判断（pKa预测） - 王少许的博文 (sciencenet.cn)

make_ndx

  • gmx_mpi make_ndx -f ref.pdb -o index.ndx
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  • > r 172-324
    • 

  • > r 49 57 58 233 333 334 336 349 389 393

rms

  • nohup sh -c 'for i in {0..27};do echo 1 14|gmx_mpi rms -s ref.pdb -f /home/databank/zzy/project/trip13/0415_500ns/vsremd20230609/500ns/cpp/0415${i}.xtc -n index.ndx -o AAA_ATPase${i}_rmsd.xvg;done' &
    • 


    • 

  • nohup sh -c 'for i in {0..27};do echo 1 1|gmx_mpi rms -s ref.pdb -f /home/databank/zzy/project/trip13/0415_500ns/vsremd20230609/500ns/cpp/0415${i}.xtc -o pro${i}_rmsd.xvg;done' &
    •

gyrate

  • nohup sh -c 'for i in {0..27};do echo 1|gmx_mpi gyrate -s ../ref.pdb -f /home/databank/zzy/project/trip13/0415_500ns/vsremd20230609/500ns/cpp/0415${i}.xtc -o gyrate_${i}.xvg;done' &                                                                                              

grompp

  • gmx_mpi grompp -f../../md0.mdp -c ../../npt0.gro -p ../../../topol/topol.top -n ../../../topol/index.ndx -o md0.tpr