Update README.md

README.md

@@ -27,70 +27,3 @@ Please cite this manuscript for papers that use the DynateinDB dataset:
 | Average system size (residues)  | ~59 |
 | Storage size  | ... |
 
-
-
-## Download GROMACS 2024.1 and configure the environment.
-
-```
-  wget https://ftp.gromacs.org/gromacs/gromacs-2024.1.tar.gz # Download GROMACS 2024.1
-  tar -xf gromacs-2024.1.tar.gz
-  cd gromacs-2024.1 
-  
-  mkdir build # Create build directory
-  cd build
-  
-  cmake .. \ # CMake configuration
-      -DGMX_BUILD_OWN_FFTW=ON \
-      -DGMX_GPU=CUDA \
-      -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-13.0 \
-      -DCMAKE_C_COMPILER=gcc \
-      -DCMAKE_CXX_COMPILER=g++
-  
-  make -j 10 # Compile and install
-  make install
-  
-  source /usr/local/gromacs/bin/GMXRC # Load GROMACS environment variables
-  echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bashrc
-```
-
-## Molecular Dynamics simulation workflow setup (Taking the 1A11.pdb protein as an example)
-
-### 1.Generate topology and initial structure（CHARMM36m）
-```
-  yes 9 | gmx pdb2gmx -f 1A11.pdb -o 1A11_processed.gro -water tip3p -ignh -missing
-```
-
-### 2.Define simulation box
-```
-  gmx editconf -f 1A11_processed.gro -o 1A11_newbox.gro -c -d 1.0 -bt cubic
-```
-### 3.Solvate system
-```
-  gmx solvate -cp 1A11_newbox.gro -cs spc216.gro -o 1A11_solv.gro -p topol.top
-```
-### 4.Add ions
-```
-  gmx grompp -f ions.mdp -c 1A11_solv.gro -p topol.top -o ions.tpr
-  echo "SOL" | gmx genion -s ions.tpr -o 1A11_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.15
-```
-### 5.Energy minimization
-```
-  gmx grompp -f minim.mdp -c 1A11_solv_ions.gro -p topol.top -o em.tpr
-  gmx mdrun -deffnm em -ntomp 15 -nb gpu -gpu_id 0
-```
-### 6.NVT equilibration
-```
-  gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
-  gmx mdrun -deffnm nvt -ntomp 15 -nb gpu -gpu_id 0
-```
-### 7.NPT equilibration
-```
-  gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
-  gmx mdrun -deffnm npt -ntomp 15 -nb gpu -gpu_id 0
-```
-### 8.Production MD
-```
-  gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
-  gmx mdrun -deffnm md_0_1 -ntomp 15 -nb gpu -gpu_id 0
-```
-