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