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lingyu zeng
2024-09-18 15:11:00 +08:00
parent ded062a855
commit 82d60391bf
3 changed files with 7454 additions and 5 deletions
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2
Dockerfile.gromacs_amber
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@@ -173,7 +173,7 @@ ENV DOWNLOAD_MINICONDA="False"
# install ambertools # install ambertools
RUN <<EOT RUN <<EOT
#!/bin/bash #!/bin/bash
python3 -m pip install https://blog.csdn.net/GHZ2443063059/article/details/141103550 python3 -m pip install numpy scipy matplotlib
# 解压 Amber24 # 解压 Amber24
tar -xjf Amber24.tar.bz2 tar -xjf Amber24.tar.bz2
# 解压 AmberTools24 # 解压 AmberTools24

7449
script/S112D-Alphafold2.pdb Normal file
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8
script/S112D.sh
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@@ -8,7 +8,7 @@
if [ -n "$GMXRC_PATH" ]; then if [ -n "$GMXRC_PATH" ]; then
source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC
fi fi
NAME=${NAME:-"5sws_fixer"} NAME=${NAME:-"S112D-Alphafold2"}
# FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"} # FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"}
FORCEFIELD=${FORCEFIELD:-"amber99sb"} FORCEFIELD=${FORCEFIELD:-"amber99sb"}
WATERMODEL=${WATERMODEL:-"tip3p"} WATERMODEL=${WATERMODEL:-"tip3p"}
@@ -138,7 +138,7 @@ fourierspacing = 0.16 ; grid spacing for FFT
tcoupl = V-rescale ; modified Berendsen thermostat tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K ref_t = 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is off ; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions ; Periodic boundary conditions
@@ -243,7 +243,7 @@ fourierspacing = 0.16 ; grid spacing for FFT
tcoupl = V-rescale ; modified Berendsen thermostat tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K ref_t = 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is on ; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors pcoupltype = isotropic ; uniform scaling of box vectors
@@ -262,7 +262,7 @@ EOF
gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE} gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}
# Run the simulation # Run the simulation
gmx_mpi mdrun -deffnm ${MDRUN_NAME} gmx_mpi mdrun -deffnm ${MDRUN_NAME} -update gpu -ntomp 1
# extra ndx file , select protein # extra ndx file , select protein
echo -e "1\nq" | gmx_mpi make_ndx -f ${MDRUN_NAME}.gro -o ${NDX_FILE} echo -e "1\nq" | gmx_mpi make_ndx -f ${MDRUN_NAME}.gro -o ${NDX_FILE}