328 lines
18 KiB
Bash
Executable File
328 lines
18 KiB
Bash
Executable File
#!/bin/bash
|
||
#This script needs to be edited for each run.
|
||
#Define PDB Filename & GROMACS Pameters
|
||
# reference: http://www.mdtutorials.com/gmx/lysozyme/
|
||
# NAME=1ao7 NSTEPS=50000000 ./md_gromacs.sh
|
||
# 命令会临时设置 NAME 为 1ao7 和 NSTEPS 为 50000000（对应 100ns），然后运行 md_gromacs.sh 脚本
|
||
# Check if GMXRC_PATH is provided and source it
|
||
if [ -n "$GMXRC_PATH" ]; then
|
||
source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC
|
||
fi
|
||
NAME=${NAME:-"5sws_fixer"}
|
||
FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"}
|
||
WATERMODEL=${WATERMODEL:-"tip3p"}
|
||
WATERTOPFILE=${WATERTOPFILE:-"spc216.gro"}
|
||
BOXTYPE=${BOXTYPE:-"tric"}
|
||
BOXORIENTATION=${BOXORIENTATION:-"1.0"}
|
||
NUM_CORES=${NUM_CORES:-$(($(nproc) - 2))} # 默认使用 CPU 核心数减去 2，如果外部有设置则使用外部值
|
||
NUM_CORES=$((NUM_CORES > 0 ? NUM_CORES : 1)) # 确保 NUM_CORES 至少为 1
|
||
NSTEPS=${NSTEPS:-500000} # 50,000 steps for 1 ns
|
||
DT=${DT:-0.002} # 2 fs
|
||
#BOXSIZE="5.0"
|
||
#BOXCENTER="2.5"
|
||
# Define simulation name variable
|
||
MDRUN_NAME=${MDRUN_NAME:-"md"}
|
||
NDX_NAME=${NDX_NAME:-"index"}
|
||
# Define analysis parameters
|
||
# Define other filenames based on MDRUN_NAME
|
||
TPR_FILE="${MDRUN_NAME}.tpr"
|
||
XTC_FILE="${MDRUN_NAME}.xtc"
|
||
NDX_FILE="${NDX_NAME}.ndx"
|
||
NO_PBC_XTC_FILE="${MDRUN_NAME}_noPBC.xtc"
|
||
OUTPUT_FOLDER=${OUTPUT_FOLDER:-"frame_extraction_output"}
|
||
TEMP_FOLDER=${TEMP_FOLDER:-"temp"}
|
||
# Define variables for frame extraction
|
||
EXTRACT_EVERY_PS=${EXTRACT_EVERY_PS:-100} # Default to 100 ps if not set
|
||
|
||
# Print the current settings
|
||
echo "Current settings:"
|
||
echo "NAME: $NAME"
|
||
echo "FORCEFIELD: $FORCEFIELD"
|
||
echo "WATERMODEL: $WATERMODEL"
|
||
echo "WATERTOPFILE: $WATERTOPFILE"
|
||
echo "BOXTYPE: $BOXTYPE"
|
||
echo "BOXORIENTATION: $BOXORIENTATION"
|
||
echo "NSTEPS: $NSTEPS"
|
||
echo "DT: $DT"
|
||
echo "MDRUN_NAME: $MDRUN_NAME"
|
||
echo "TPR_FILE: $TPR_FILE"
|
||
echo "XTC_FILE: $XTC_FILE"
|
||
echo "NO_PBC_XTC_FILE: $NO_PBC_XTC_FILE"
|
||
echo "OUTPUT_FOLDER: $OUTPUT_FOLDER"
|
||
echo "EXTRACT_EVERY_PS: $EXTRACT_EVERY_PS"
|
||
echo "NUM_CORES: $NUM_CORES"
|
||
|
||
# 函数：打印步骤信息和运行命令
|
||
run_command() {
|
||
local step_description=$1
|
||
local command=$2
|
||
|
||
echo "Starting: $step_description"
|
||
echo "Command: $command"
|
||
eval $command
|
||
local status=$?
|
||
|
||
if [ $status -ne 0 ]; then
|
||
echo "Error in $step_description. Command: $command"
|
||
exit $status
|
||
fi
|
||
echo "Completed: \n $step_description"
|
||
}
|
||
|
||
# generate GROMACS .gro file
|
||
run_command "Generating GROMACS .gro file" "mpirun -np $NUM_CORES gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -ignh -p topol.top"
|
||
# define the box
|
||
run_command "Defining the box" "mpirun -np $NUM_CORES gmx_mpi editconf -f $NAME.gro -o $NAME-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION"
|
||
# add solvate
|
||
run_command "Adding solvate" "mpirun -np $NUM_CORES gmx_mpi solvate -cp $NAME-box.gro -cs $WATERTOPFILE -o $NAME-solv.gro -p topol.top"
|
||
# add icons # ! ions.mdp add by manual
|
||
# --- ions.mdp file content --- #
|
||
cat << EOF > ions.mdp
|
||
; ions.mdp - used as input into grompp to generate ions.tpr
|
||
; Parameters describing what to do, when to stop and what to save
|
||
integrator = steep ; Algorithm （steep = steepest descent minimization）
|
||
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
|
||
emstep = 0.01 ; Minimization step size
|
||
nsteps = 50000 ; Maximum number of （minimization） steps to perform
|
||
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
|
||
nstlist = 1 ; Frequency to update the neighbor list and long range forces
|
||
cutoff-scheme = Verlet ; Buffered neighbor searching
|
||
ns_type = grid ; Method to determine neighbor list （simple, grid）
|
||
coulombtype = cutoff ; Treatment of long range electrostatic interactions
|
||
rcoulomb = 1.0 ; Short-range electrostatic cut-off
|
||
rvdw = 1.0 ; Short-range Van der Waals cut-off
|
||
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
|
||
EOF
|
||
run_command "Adding ions" "mpirun -np $NUM_CORES gmx_mpi grompp -f ions.mdp -c $NAME-solv.gro -p topol.top -o ions.tpr -maxwarn 1"
|
||
# echo "SOL" > ions_input.txt
|
||
# mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral < ions_input.txt
|
||
run_command "Generating ions" "echo 'SOL' | mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral"
|
||
# energy minimization of the structure in solvate # ! minim.mdp add by manual
|
||
# --- minim.mdp file content --- #
|
||
cat << EOF > minim.mdp
|
||
; minim.mdp - used as input into grompp to generate em.tpr
|
||
; Parameters describing what to do, when to stop and what to save
|
||
integrator = steep ; Algorithm （steep = steepest descent minimization）
|
||
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
|
||
emstep = 0.01 ; Minimization step size
|
||
nsteps = 50000 ; Maximum number of （minimization） steps to perform
|
||
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
|
||
nstlist = 1 ; Frequency to update the neighbor list and long range forces
|
||
cutoff-scheme = Verlet ; Buffered neighbor searching
|
||
ns_type = grid ; Method to determine neighbor list （simple, grid）
|
||
coulombtype = PME ; Treatment of long range electrostatic interactions
|
||
rcoulomb = 1.0 ; Short-range electrostatic cut-off
|
||
rvdw = 1.0 ; Short-range Van der Waals cut-off
|
||
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
|
||
EOF
|
||
run_command "Energy minimization" "mpirun -np $NUM_CORES gmx_mpi grompp -f minim.mdp -c $NAME-solv-ions.gro -p topol.top -o em.tpr"
|
||
run_command "Running energy minimization" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm em"
|
||
# optional em, you will need the Xmgrace plotting too
|
||
#gmx_mpi energy -f em.edr -o potential.xvg
|
||
#position restrain
|
||
# gmx_mpi grompp -f posre.mdp -c em.gro -p topol.top -o posre.tpr -r em.gro
|
||
# gmx_mpi mdrun -v -deffnm posre
|
||
# nvt
|
||
# gmx_mpi grompp -f nvt.mdp -c posre.gro -p topol.top -o nvt.tpr
|
||
# --- nvt.mdp file content --- #
|
||
cat << EOF > nvt.mdp
|
||
title = OPLS Lysozyme NVT equilibration
|
||
define = -DPOSRES ; position restrain the protein
|
||
; Run parameters
|
||
integrator = md ; leap-frog integrator
|
||
nsteps = 50000 ; 2 * 50000 = 100 ps
|
||
dt = 0.002 ; 2 fs
|
||
; Output control
|
||
nstxout = 500 ; save coordinates every 1.0 ps
|
||
nstvout = 500 ; save velocities every 1.0 ps
|
||
nstenergy = 500 ; save energies every 1.0 ps
|
||
nstlog = 500 ; update log file every 1.0 ps
|
||
; Bond parameters
|
||
continuation = no ; first dynamics run
|
||
constraint_algorithm = lincs ; holonomic constraints
|
||
constraints = h-bonds ; bonds involving H are constrained
|
||
lincs_iter = 1 ; accuracy of LINCS
|
||
lincs_order = 4 ; also related to accuracy
|
||
; Nonbonded settings
|
||
cutoff-scheme = Verlet ; Buffered neighbor searching
|
||
ns_type = grid ; search neighboring grid cells
|
||
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
|
||
rcoulomb = 1.0 ; short-range electrostatic cutoff （in nm）
|
||
rvdw = 1.0 ; short-range van der Waals cutoff （in nm）
|
||
DispCorr = EnerPres ; account for cut-off vdW scheme
|
||
; Electrostatics
|
||
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
|
||
pme_order = 4 ; cubic interpolation
|
||
fourierspacing = 0.16 ; grid spacing for FFT
|
||
; Temperature coupling is on
|
||
tcoupl = V-rescale ; modified Berendsen thermostat
|
||
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
|
||
tau_t = 0.1 0.1 ; time constant, in ps
|
||
ref_t = 300 300 ; reference temperature, one for each group, in K
|
||
; Pressure coupling is off
|
||
pcoupl = no ; no pressure coupling in NVT
|
||
; Periodic boundary conditions
|
||
pbc = xyz ; 3-D PBC
|
||
; Velocity generation
|
||
gen_vel = yes ; assign velocities from Maxwell distribution
|
||
gen_temp = 300 ; temperature for Maxwell distribution
|
||
gen_seed = -1 ; generate a random seed
|
||
EOF
|
||
run_command "Preparing NVT simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr"
|
||
run_command "Running NVT simulation" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm nvt"
|
||
# optional : Let's analyze the temperature progression, again using energy:
|
||
# gmx_mpi energy -f nvt.edr -o temperature.xvg
|
||
# npt
|
||
# gmx_mpi grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
|
||
# --- npt.mdp file content --- #
|
||
cat << EOF > npt.mdp
|
||
title = OPLS Lysozyme NPT equilibration
|
||
define = -DPOSRES ; position restrain the protein
|
||
; Run parameters
|
||
integrator = md ; leap-frog integrator
|
||
nsteps = 50000 ; 2 * 50000 = 100 ps
|
||
dt = 0.002 ; 2 fs
|
||
; Output control
|
||
nstxout = 500 ; save coordinates every 1.0 ps
|
||
nstvout = 500 ; save velocities every 1.0 ps
|
||
nstenergy = 500 ; save energies every 1.0 ps
|
||
nstlog = 500 ; update log file every 1.0 ps
|
||
; Bond parameters
|
||
continuation = yes ; Restarting after NVT
|
||
constraint_algorithm = lincs ; holonomic constraints
|
||
constraints = h-bonds ; bonds involving H are constrained
|
||
lincs_iter = 1 ; accuracy of LINCS
|
||
lincs_order = 4 ; also related to accuracy
|
||
; Nonbonded settings
|
||
cutoff-scheme = Verlet ; Buffered neighbor searching
|
||
ns_type = grid ; search neighboring grid cells
|
||
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
|
||
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
|
||
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
|
||
DispCorr = EnerPres ; account for cut-off vdW scheme
|
||
; Electrostatics
|
||
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
|
||
pme_order = 4 ; cubic interpolation
|
||
fourierspacing = 0.16 ; grid spacing for FFT
|
||
; Temperature coupling is on
|
||
tcoupl = V-rescale ; modified Berendsen thermostat
|
||
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
|
||
tau_t = 0.1 0.1 ; time constant, in ps
|
||
ref_t = 300 300 ; reference temperature, one for each group, in K
|
||
; Pressure coupling is on
|
||
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
|
||
pcoupltype = isotropic ; uniform scaling of box vectors
|
||
tau_p = 2.0 ; time constant, in ps
|
||
ref_p = 1.0 ; reference pressure, in bar
|
||
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
|
||
refcoord_scaling = com
|
||
; Periodic boundary conditions
|
||
pbc = xyz ; 3-D PBC
|
||
; Velocity generation
|
||
gen_vel = no ; Velocity generation is off
|
||
EOF
|
||
run_command "Preparing NPT simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr"
|
||
run_command "Running NPT simulation" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm npt"
|
||
# Optional: Let's analyze the pressure progression, again using energy: type 18 0
|
||
# gmx energy -f npt.edr -o pressure.xvg
|
||
# Optional: Let's take a look at density as well, this time using energy and entering "24 0" at the prompt.
|
||
# gmx energy -f npt.edr -o density.xvg
|
||
# md
|
||
# --- md.mdp file content --- #
|
||
cat << EOF > ${MDRUN_NAME}.mdp
|
||
title = OPLS Lysozyme NPT equilibration
|
||
; Run parameters
|
||
integrator = md ; leap-frog integrator
|
||
nsteps = ${NSTEPS} ; steps for simulation
|
||
dt = ${DT} ; time step in fs
|
||
; Output control
|
||
nstxout = 0 ; suppress bulky .trr file by specifying
|
||
nstvout = 0 ; 0 for output frequency of nstxout,
|
||
nstfout = 0 ; nstvout, and nstfout
|
||
nstenergy = 5000 ; save energies every 10.0 ps
|
||
nstlog = 5000 ; update log file every 10.0 ps
|
||
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
|
||
compressed-x-grps = System ; save the whole system
|
||
; Bond parameters
|
||
continuation = yes ; Restarting after NPT
|
||
constraint_algorithm = lincs ; holonomic constraints
|
||
constraints = h-bonds ; bonds involving H are constrained
|
||
lincs_iter = 1 ; accuracy of LINCS
|
||
lincs_order = 4 ; also related to accuracy
|
||
; Neighborsearching
|
||
cutoff-scheme = Verlet ; Buffered neighbor searching
|
||
ns_type = grid ; search neighboring grid cells
|
||
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
|
||
rcoulomb = 1.0 ; short-range electrostatic cutoff （in nm）
|
||
rvdw = 1.0 ; short-range van der Waals cutoff （in nm）
|
||
; Electrostatics
|
||
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
|
||
pme_order = 4 ; cubic interpolation
|
||
fourierspacing = 0.16 ; grid spacing for FFT
|
||
; Temperature coupling is on
|
||
tcoupl = V-rescale ; modified Berendsen thermostat
|
||
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
|
||
tau_t = 0.1 0.1 ; time constant, in ps
|
||
ref_t = 300 300 ; reference temperature, one for each group, in K
|
||
; Pressure coupling is on
|
||
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
|
||
pcoupltype = isotropic ; uniform scaling of box vectors
|
||
tau_p = 2.0 ; time constant, in ps
|
||
ref_p = 1.0 ; reference pressure, in bar
|
||
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
|
||
; Periodic boundary conditions
|
||
pbc = xyz ; 3-D PBC
|
||
; Dispersion correction
|
||
DispCorr = EnerPres ; account for cut-off vdW scheme
|
||
; Velocity generation
|
||
gen_vel = no ; Velocity generation is off
|
||
EOF
|
||
|
||
# Generate GROMACS .tpr file for the simulation
|
||
run_command "Preparing MD simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}"
|
||
# Run the simulation
|
||
mpirun -np ${NUM_CORES} gmx_mpi mdrun -deffnm ${MDRUN_NAME} -update gpu -ntomp 1
|
||
# mpirun -np $(ls | egrep "Scaled[0-9]+$" | wc -l) gmx_mpi mdrun -v --deffnm md -cpi Scaled.cpt -multidir $(ls -v | egrep "Scaled[0-9]+$") -plumed plumed.dat -hrex -replex 1000 >& run_$(date "+%H%M%S_%d%m%Y").log || { echo "mdrun failed at line ${LINENO} "; exit -1; }
|
||
# 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 md.gro -o index.ndx
|
||
|
||
# Create extraction output directory Create temp output directory
|
||
run_command "Creating output directories" "mkdir -p ${OUTPUT_FOLDER} && mkdir -p ${TEMP_FOLDER}"
|
||
|
||
run_command "Extracting frames" "echo -e '1\nq' | gmx_mpi trjconv -dt ${EXTRACT_EVERY_PS} -s ${TPR_FILE} -f ${XTC_FILE} -n ${NDX_FILE} -pbc mol -o ${TEMP_FOLDER}/temp.xtc"
|
||
run_command "Centering and fitting trajectory" "echo -e '1\n1\n1' | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -o ${TEMP_FOLDER}/traj_show.xtc"
|
||
run_command "Generating PDB file" "echo -e '1\n1\n1' | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -b 0 -e 0 -o ${TEMP_FOLDER}/tarj_show.pdb"
|
||
|
||
# Group 1 ( Protein)
|
||
|
||
|
||
# Continue with further analysis like RMSD calculation...
|
||
# ... [other analysis commands] ...
|
||
|
||
# End of script
|
||
|
||
# command reference
|
||
|
||
# Command 1: 提取蛋白质
|
||
# command_1 = f'echo "Protein" | gmx trjconv -dt 1000 -s {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
|
||
# echo "Protein": 选择蛋白质组，用于告诉 gmx trjconv 要处理哪个部分。
|
||
# -dt 1000: 指定时间间隔（这里是1000 picoseconds），用于从 .xtc 文件中抽取帧。
|
||
# -s {tpr_file}: 指定拓扑文件（.tpr），它包含了模拟系统的完整描述。
|
||
# -f {xtc_file}: 指定原始的 .xtc 轨迹文件。
|
||
# -n {temp_folder}/tarj_show.ndx: 指定索引文件，其中包含各种原子群的定义。
|
||
# -pbc mol: 处理周期性边界条件，确保分子不会被分割。
|
||
# -o {temp_folder}/temp.xtc: 指定输出文件名和位置。
|
||
# Command 2: 中心对齐蛋白质
|
||
# command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc'
|
||
# echo "Protein\nProtein\nProtein": 三次选择蛋白质组，分别用于中心化、拟合和输出。
|
||
# -center: 将蛋白质移动到框架的中心。
|
||
# -fit rot+trans: 对齐蛋白质，通过旋转和平移来最佳拟合。
|
||
# -o {output_folder}/traj_show.xtc: 指定输出文件名和位置。
|
||
# Command 3: 抽取帧生成 .pdb 文件
|
||
# command_3 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {output_folder}/tarj_show.pdb'
|
||
# -b 0 -e 0: 指定开始和结束时间，这里设置为0表示只取第一帧。
|
||
# -o {output_folder}/tarj_show.pdb: 输出为 .pdb 格式，存储在指定的位置。
|
||
|
||
# 调用更多GPU负载用法
|
||
# mpirun -np 32 gmx_mpi mdrun -deffnm md4 -update gpu -ntomp 1 |