计算MMGBSA

最好单独建一个文件夹，会输出很多文件
nohup mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o mmgbsa.dat -cp native.prmtop -rp pro.prmtop -lp lig.prmtop -y dry-align.xtc -eo mmgbsa.csv &


awk -F ' ' '$28<-1 {print}' FINAL_DECOMP_MMPBSA.dat

1:
nohup mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o mmgbsa.dat -cp ../../complex/native.prmtop -rp ../../complex/pro.prmtop -lp ../../complex/lig.prmtop -y ../pbc-auto.xtc -eo mmgbsa.csv &




2:
nohup mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o mmgbsa.dat -cp ../../complex/native.prmtop -rp ../../complex/pro.prmtop -lp ../../complex/lig.prmtop -y ../pbc-auto.xtc -eo mmgbsa.csv &




3:
nohup mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o mmgbsa.dat -cp ../../complex/native.prmtop -rp ../../complex/pro.prmtop -lp ../../complex/lig.prmtop -y ../pbc-auto.xtc -eo mmgbsa.csv &




5:
nohup mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o mmgbsa.dat -cp ../../complex/native.prmtop -rp ../../complex/pro.prmtop -lp ../../complex/lig.prmtop -y ../pbc-auto.xtc -eo mmgbsa.csv &

source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
> parm "/home/data/pengziyu/0106/md-4zy4/0108-4zy4-3/complex/native.prmtop"
> trajin pbc.xtc
> autoimage
> rms
> trajout pbc-align.xtc 
> run
source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-align.xtc -s md.tpr -n index.ndx -o rmsd-protein.xvg
可视化
source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
parm "/home/data/pengziyu/0106/md-4zy4/0108-4zy4-3/complex/complex.prmtop"
trajin pbc.xtc 1 10000000000 1000
rms
trajout check.pdb 
run


1:mmgbsa2
nohup mpirun -np 50 MMPBSA.py.MPI -O -i mmgbsa.in -o mmgbsa.dat -cp ../../complex/native.prmtop -rp ../../complex/pro.prmtop -lp ../../complex/lig.prmtop -y pbc-align.xtc -eo mmgbsa.csv &