big update
This commit is contained in:
root
@@ -10,13 +10,14 @@ if [ -n "$GMXRC_PATH" ]; then
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fi
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GPU_ID=${GPU_ID:-"0"}
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LIGAND_GRO="ligand.gro" # 配体的 .gro 文件
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LIGAND_ITP="ligand.itp" # 配体的 .itp 文件
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NAME="protein"
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LIGAND_GRO="mole.gro" # 配体的 .gro 文件
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LIGAND_ITP="mole.itp" # 配体的 .itp 文件
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# FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"}
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FORCEFIELD=${FORCEFIELD:-"amber99sb"}
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WATERMODEL=${WATERMODEL:-"tip3p"}
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WATERTOPFILE=${WATERTOPFILE:-"spc216.gro"}
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BOXTYPE=${BOXTYPE:-"tric"}
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BOXTYPE=${BOXTYPE:-"tric"} # or dodecahedron
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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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NSTEPS=${NSTEPS:-50000000} # 100 ns 模拟
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@@ -62,11 +63,11 @@ gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -p
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# 使用 Sobtop（http://sobereva.com/soft/Sobtop）提取
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# Step 2: Merge protein and ligand .gro files into a complex
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cat $NAME.gro mol.gro > complex.gro
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cat $NAME.gro mole.gro > complex.gro
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# 获取蛋白质和小分子的原子数
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PROTEIN_ATOMS=$(head -n 2 $NAME.gro | tail -n 1 | tr -d ' ')
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LIGAND_ATOMS=$(head -n 2 mol.gro | tail -n 1 | tr -d ' ')
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LIGAND_ATOMS=$(head -n 2 mole.gro | tail -n 1 | tr -d ' ')
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# 打印原子数，确保正确
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echo "Protein atoms: $PROTEIN_ATOMS"
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@@ -75,41 +76,23 @@ echo "Ligand atoms: $LIGAND_ATOMS"
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# 计算总原子数
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TOTAL_ATOMS=$(($PROTEIN_ATOMS + $LIGAND_ATOMS))
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# 打印总原子数
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# 打印总原子数 7482
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echo "Total atoms: $TOTAL_ATOMS"
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# Update the atom count in the complex.gro file
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# 更新原子数目 # ! 手动实现
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sed -i "2s/\(^[[:space:]]*\)[0-9]\+/\1$TOTAL_ATOMS/" complex.gro
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echo -e "0\nq" | gmx_mpi genrestr -f mol.gro -o posre_mol.itp
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cat << EOF >> mol.itp
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#ifdef POSRES
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#include "posre_mol.itp"
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#endif
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EOF
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# Modify the topology file to include the ligand
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# echo "#include \"$LIGAND_ITP\"" >> topol.top
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# Step 6: Modify the topology file to include the ligand and its parameters
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# 6.1 在topol.top顶部添加小分子的参数文件
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sed -i '/^; Include forcefield parameters/a #include "jz4.prm"' topol.top
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# 6.2 在position restraint后添加小分子的拓扑文件
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sed -i '/^; Include Position restraint file/!b;n;/#endif/a ; Include ligand topology\n#include "jz4.itp"' topol.top
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# 6.3 在[molecules]部分添加小分子
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sed -i '/^Protein_chain_A/a JZ4 1' topol.top
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# 定义盒子、添加溶剂和离子、能量最小化
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# 定义盒子并向盒子充满水
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# Step 3: Define the simulation box
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gmx_mpi editconf -f complex.gro -o complex-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION
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# gmx_mpi editconf -f complex.gro -o complex-box.gro -bt dodecahedron -c -d 1.0
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# Step 4: Add solvate
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gmx_mpi solvate -cp complex-box.gro -cs $WATERTOPFILE -o complex-solv.gro -p topol.top
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# gmx_mpi solvate -cp complex-box.gro -cs spc216.gro -o complex-solv.gro -p topol.top
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# 添加离子
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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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@@ -129,7 +112,14 @@ 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 complex-solv.gro -p topol.top -o ions.tpr -maxwarn 1
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# 添加NaCl
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echo SOL | gmx_mpi genion -s ions.tpr -o complex-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral
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# -pname 阳离子的名称
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# -nname 阴离子的名称
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# -np 阳离子个数
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# -nn 阴离子个数
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# 能量最小化
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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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@@ -150,46 +140,117 @@ 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 complex-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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# 查看系统的系统的总势能变化情况
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echo "12\n" | gmx_mpi energy -f em.edr -o potential.xvg
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# 系统的总势能变化绘图
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./plot_potential.sh potential.xvg potential.svg
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# 位置约束（Position Restraint）
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# 位置约束是指在进行模拟时，约束某些原子的位置，使它们不会偏离初始坐标。在能量最小化之后的位置约束步骤用于对溶剂和其他环境进行平衡，同时保持蛋白质或其他分子的位置不变。通常用于溶液系统的准备过程，以避免对生物分子结构造成过大影响。
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# 位置约束步骤解释
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# posre.mdp 文件是位置约束的输入文件，它会约束特定原子的运动。
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# grompp -r em.gro：此命令中的 -r em.gro 参数指明位置约束应基于已经能量最小化的结构 em.gro 进行。
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# mdrun -deffnm posre：执行模拟时，会生成位置约束下的模拟结果。
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# 如何使用
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# 首先准备好 posre.mdp 文件，然后执行以下命令：
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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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# 这将生成一个应用位置约束后的系统，用于后续的分子动力学模拟步骤。
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# 位置限制的目的: 加速体系平衡, 减少计算资源浪费
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# 对配体施加位置限制（position restraint），通常是为了在分子动力学模拟的早期阶段保持配体在特定位置，以帮助系统更快达到平衡，尤其是在 NVT（恒体积恒温）和 NPT（恒压恒温）平衡的过程中。这种约束有助于避免在系统能量未平衡时，配体位置大幅偏离而影响蛋白-配体复合物的稳定性。
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# 位置限制通常在以下情况中使用：
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# 能量最小化后，NVT 和 NPT 平衡之前：
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# 在模拟的平衡阶段（NVT 和 NPT），施加配体限制可以保证配体在溶剂环境中不产生大幅度的偏移，特别是在系统温度和压力稳定之前。这时配体的限制作用是关键的。
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# 平衡后，生产阶段去除限制：
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# 在生产阶段（即实际的分子动力学生产模拟），通常应去除位置限制，以观察蛋白-配体复合物的真实动态行为。如果限制保留在生产阶段，配体的运动将受到不必要的约束，无法得到真实的配体运动轨迹。
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# 限制可做可不做的情况：
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# 如果体系比较简单，且配体与蛋白质的相互作用较强，位置限制可以选择不做，直接让配体在系统中自由运动。
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# 如果配体是比较松散或弱结合到蛋白质上的，或者你关心配体的初期运动轨迹，初期的短时间平衡阶段可以不施加限制。
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# 限制配体
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# 平衡蛋白配体复合物与平衡水中只包含蛋白的体系非常类似，值得注意的是：
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# 1、对配体施加限定。
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# 2、对于温度耦合群的处理。
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# 为了限定配体，需要为他生成一个位置限定拓扑。首先，为JZ4创建一个只包含非氢原子的index group。
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gmx_mpi make_ndx -f mole.gro -o index_mole.ndx << EOF
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0 & ! a H*
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q
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EOF
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# 执行genrestr模块，选择新创建的index group（在index_mole.ndx文件中是group 3）
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# echo -e "0\nq" | gmx_mpi genrestr -f mol.gro -o posre_mol.itp
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gmx_mpi genrestr -f mole.gro -n index_mole.ndx -o posre_mole.itp -fc 1000 1000 1000 << EOF
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3
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EOF
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# 下一步需要把这个信息包括在拓扑文件中。有几种方式，取决于我们希望使用的条件。这里介绍第一种：如果我们想在无论蛋白是否被限定的条件下对配体施加限定，在拓扑文件的Include ligand topology之后中加入如下内容：
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# 在拓扑文件的Include ligand topology之后中加入如下内容
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: << EOF
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; Ligand position restraints
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#ifdef POSRES
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#include "posre_mole.itp"
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#endif
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EOF
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# 必须要把限定这段话加在Include ligand topology之后，Include water topology之前，加在其他任何地方都会报错。
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# 由于对只有几个原子的组在控制其动能的涨落时, 温度耦合算法不够稳定，不要对体系中的每一单个物种使用独立的耦合。创建一个特殊的组, 其中包含蛋白质和配体。
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gmx_mpi make_ndx -f em.gro -o index.ndx << EOF
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1 | 13
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q
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EOF
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# NVT、NPT平衡
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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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title = Protein-ligand complex NVT equilibration
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define = -DPOSRES ; position restrain the protein and ligand
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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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nstxout-compressed = 500 ; save coordinates 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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; Neighbor searching and vdW
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cutoff-scheme = Verlet
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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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nstlist = 20 ; largely irrelevant with Verlet
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rlist = 1.2
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vdwtype = cutoff
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vdw-modifier = force-switch
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rvdw-switch = 1.0
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rvdw = 1.2 ; 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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rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
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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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tc-grps = Protein_MOL Water_and_ions ; 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 = 310 310 ; reference temperature, one for each group, in K
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; Pressure coupling is off
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@@ -201,118 +262,156 @@ gen_vel = yes ; assign velocities from Maxwell distributio
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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 grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr -n index.ndx
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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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# 提取并保存温度数据
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gmx_mpi energy -f nvt.edr -o temperature.xvg << EOF
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17 39 40
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EOF
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# 拆分 .xvg 文件
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# 提取整体温度
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grep -v '^@' temperature.xvg | grep -v '^#' | awk '{print $1, $2}' > system_temperature.xvg
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# 提取 Protein_MOL 组的温度
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grep -v '^@' temperature.xvg | grep -v '^#' | awk '{print $1, $3}' > protein_mol_temperature.xvg
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# 提取 Water_and_ions 组的温度
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grep -v '^@' temperature.xvg | grep -v '^#' | awk '{print $1, $4}' > water_and_ions_temperature.xvg
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# 绘制温度变化曲线
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./plot_potential.sh system_temperature.xvg system_temperature.svg
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./plot_potential.sh protein_mol_temperature.xvg protein_mol_temperature.svg
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./plot_potential.sh water_and_ions_temperature.xvg water_and_ions_temperature.svg
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# NPT平衡
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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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title = Protein-ligand complex NPT equilibration
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define = -DPOSRES ; position restrain the protein and ligand
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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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nstxout-compressed = 500 ; save coordinates every 1.0 ps
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; Bond parameters
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continuation = yes ; Restarting after NVT
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continuation = yes ; continuing from 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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constraints = h-bonds ; bonds to 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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; Neighbor searching and vdW
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cutoff-scheme = Verlet
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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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nstlist = 20 ; largely irrelevant with Verlet
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rlist = 1.2
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vdwtype = cutoff
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vdw-modifier = force-switch
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rvdw-switch = 1.0
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rvdw = 1.2 ; 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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rcoulomb = 1.2
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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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; Temperature coupling
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tcoupl = V-rescale ; modified Berendsen thermostat
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tc-grps = Protein_MOL Water_and_ions ; 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
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pcoupl = Parrinello-Rahman ; Parrinello-Rahman or C-rescale for NPT production
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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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; Dispersion correction is not used for proteins with the C36 additive FF
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DispCorr = no
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; Velocity generation
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gen_vel = no ; Velocity generation is off
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gen_vel = no ; velocity generation off after NVT
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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
|
||||
gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -n index.ndx
|
||||
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
|
||||
gmx_mpi energy -f npt.edr -o pressure.xvg << EOF
|
||||
18
|
||||
0
|
||||
EOF
|
||||
|
||||
# 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
|
||||
gmx_mpi energy -f npt.edr -o density.xvg << EOF
|
||||
24
|
||||
0
|
||||
EOF
|
||||
|
||||
# 绘制 SVG 图像
|
||||
# 绘制压力图像
|
||||
./plot_potential.sh pressure.xvg pressure.svg
|
||||
|
||||
# 绘制密度图像
|
||||
./plot_potential.sh density.xvg density.svg
|
||||
|
||||
# md
|
||||
# --- md.mdp file content --- #
|
||||
cat << EOF > ${MDRUN_NAME}.mdp
|
||||
title = OPLS Lysozyme NPT equilibration
|
||||
title = Protein-ligand complex MD simulation
|
||||
; Run parameters
|
||||
integrator = md ; leap-frog integrator
|
||||
nsteps = ${NSTEPS} ; steps for simulation
|
||||
dt = ${DT} ; time step in fs
|
||||
nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)
|
||||
dt = 0.002 ; 2 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
|
||||
nstxout-compressed = 5000 ; save coordinates every 10.0 ps
|
||||
; Bond parameters
|
||||
continuation = yes ; Restarting after NPT
|
||||
constraint_algorithm = lincs ; holonomic constraints
|
||||
constraints = h-bonds ; bonds involving H are constrained
|
||||
continuation = yes ; continuing from NPT
|
||||
constraint_algorithm = lincs ; holonomic constraints
|
||||
constraints = h-bonds ; bonds to H are constrained
|
||||
lincs_iter = 1 ; accuracy of LINCS
|
||||
lincs_order = 4 ; also related to accuracy
|
||||
; Neighborsearching
|
||||
cutoff-scheme = Verlet ; Buffered neighbor searching
|
||||
; Neighbor searching and vdW
|
||||
cutoff-scheme = Verlet
|
||||
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）
|
||||
nstlist = 20 ; largely irrelevant with Verlet
|
||||
rlist = 1.2
|
||||
vdwtype = cutoff
|
||||
vdw-modifier = force-switch
|
||||
rvdw-switch = 1.0
|
||||
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
|
||||
; Electrostatics
|
||||
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
|
||||
rcoulomb = 1.2
|
||||
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 = 310 310 ; 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
|
||||
; Temperature coupling
|
||||
tcoupl = V-rescale ; modified Berendsen thermostat
|
||||
tc-grps = Protein_MOL Water_and_ions ; two coupling groups - more accurate
|
||||
tau_t = 0.1 0.1 ; time constant, in ps
|
||||
ref_t = 310 310 ; reference temperature, one for each group, in K
|
||||
; Pressure coupling
|
||||
pcoupl = Parrinello-Rahman ; pressure coupling is on for 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
|
||||
; Dispersion correction is not used for proteins with the C36 additive FF
|
||||
DispCorr = no
|
||||
; Velocity generation
|
||||
gen_vel = no ; Velocity generation is off
|
||||
gen_vel = no ; continuing from NPT equilibration
|
||||
EOF
|
||||
|
||||
# Generate GROMACS .tpr file for the simulation
|
||||
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} -n index.ndx
|
||||
|
||||
# Run the simulation
|
||||
gmx_mpi mdrun -deffnm ${MDRUN_NAME} -update gpu -ntomp 1 -gpu_id ${GPU_ID}
|
||||
|
||||
Reference in New Issue
Block a user