MD轨迹-计算RMSD

#- o 参数文件可以使用第一帧蛋白ref.pdb，也可使用md.tpr,md.gro
#-pbc参数文件可以使用mol
gmx_mpi make_ndx -f ../md.gro -o index.ndx
echo 19|gmx_mpi trjconv -s ../md.tpr -f ../md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 19|gmx_mpi trjconv -s ../md.tpr -f ../md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact


-o ref.pdb 和 -o pbc.xtc 的区别： 
-o ref.pdb：输出单一帧的结构数据，以 PDB 格式保存，用于查看特定时刻的分子结构。
-o pbc.xtc：输出轨迹文件中的 所有帧，以 XTC 格式保存，用于存储和分析模拟的动态轨迹数据。  


source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
>parm ref.pdb 
>trajin pbc.xtc 
>autoimage 
>trajout pbc-auto.xtc
>run 


gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg


awk 'NR > 18 {print $1,$2}' rmsd-protein.xvg > data.txt

2：成功
gmx_mpi make_ndx -f 2/md.gro -o index.ndx
>1|13|14
echo 19|gmx_mpi trjconv -s 2/md.tpr -f 2/md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 19|gmx_mpi trjconv -s 2/md.tpr -f 2/md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact


source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
>parm ref.pdb 
>trajin pbc.xtc 
>autoimage 
>trajout pbc-auto.xtc 
>run  


source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg






1：
gmx_mpi make_ndx -f 1/md.gro -o index_pro-mol-sep.ndx
>1|13|14
echo 19|gmx_mpi trjconv -s 1/md.tpr -f 1/md.xtc -n index_pro-mol-sep.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 19|gmx_mpi trjconv -s 1/md.tpr -f 1/md.xtc -n index_pro-mol-sep.ndx -o pbc.xtc -pbc mol -ur compact


source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
>parm ref.pdb 
>trajin pbc.xtc 
>autoimage 
>trajout pbc-auto.xtc
>run  


source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg






3：
gmx_mpi make_ndx -f 1/md.gro -o index.ndx
>1|13|14
echo 19|gmx_mpi trjconv -s 3/md.tpr -f 3/md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 19|gmx_mpi trjconv -s 3/md.tpr -f 3/md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact


source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
>parm ref.pdb 
>trajin pbc.xtc 
>autoimage 
>trajout pbc-auto.xtc
>run  


source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg

实验记录：analysis-4zy4 参数文件使用pdb，结果用于计算rmsd

1:
gmx_mpi make_ndx -f md.gro -o index.ndx
>1|13
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact
source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
>parm ref.pdb 
>trajin pbc.xtc 
>autoimage 
>trajout pbc-auto.xtc
>run  
source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg


可视化
source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
> parm ref.pdb
>trajin pbc.xtc 1 10000000000 1000
>rms
>trajout check.pdb 
> run
# pymol 里看check.pdb


2:
gmx_mpi make_ndx -f md.gro -o index.ndx
>1|13
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact
source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
>parm ref.pdb 
>trajin pbc.xtc 
>autoimage 
>trajout pbc-auto.xtc
>run  
source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg
"WARNING: If there are molecules in the input trajectory file
         that are broken across periodic boundaries, they
         cannot be made whole (or treated as whole) without
         you providing a run input file.


Last frame     100000 time 200000.000


GROMACS reminds you: "I Got a Forty Dollar Bill" (F. Zappa)"


3:
gmx_mpi make_ndx -f md.gro -o index.ndx
>1|13
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact
source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
parm ref.pdb 
trajin pbc.xtc 
autoimage 
trajout pbc-auto.xtc
run  
source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg


可视化
source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
parm ref.pdb
trajin pbc.xtc 1 10000000000 1000
rms
trajout check.pdb 
run
# pymol 里看check.pdb 蛋白出界


4:
gmx_mpi make_ndx -f md.gro -o index.ndx
>1|13
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact
source ~/.gmx-cpptraj.sh 
cpptraj.OMP 
parm ref.pdb 
trajin pbc.xtc 
autoimage 
trajout pbc-auto.xtc
run  
source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg


5:
gmx_mpi make_ndx -f md.gro -o index.ndx
>1|13
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 18|gmx_mpi trjconv -s md.tpr -f md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact
source ~/.gmx-cpptraj.sh 
cpptraj.OMP
parm ref.pdb 
trajin pbc.xtc 
autoimage 
trajout pbc-auto.xtc
run  
source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg

第一次：失败
gmx_mpi make_ndx -f ../md.gro -o index.ndx
echo 19|gmx_mpi trjconv -s ../md.tpr -f ../md.xtc -n index.ndx -o ref.pdb -pbc mol -ur compact -dump 0
echo 19|gmx_mpi trjconv -s ../md.tpr -f ../md.xtc -n index.ndx -o pbc.xtc -pbc mol -ur compact
source ~/.gmx-cpptraj.sh 


cpptraj.OMP 
>parm ref.pdb 
Warning: Determining bond length parameters from element types for 'ref.pdb'.
>trajin pbc.xtc 
Warning: Trajectory box type is 'Orthorhombic' but topology box type is 'None'.
Warning: Setting topology box information from trajectory.
>autoimage 
>trajout pbc-auto.xtc
Internal Error: TrajoutList::AddTrajout() called with empty filename. 
>run  


source ~/.gmx-2022.5-GPU.sh
gmx_mpi rms -f pbc-auto.xtc -s ref.pdb -n index.ndx -o rmsd-protein.xvg


WARNING: If there are molecules in the input trajectory file
         that are broken across periodic boundaries, they
         cannot be made whole (or treated as whole) without
         you providing a run input file.


Reading frame       0 time    0.000
-------------------------------------------------------
Program:     gmx rms, version 2022.5
Source file: src/gromacs/linearalgebra/nrjac.cpp (line 164)


Fatal error:
Error: Too many iterations in routine JACOBI


For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.


NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
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