GROMACS(5.1.4)教程：蛋白质配体复合物
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蛋白质配体复合物模拟npt平衡过程中需要用到输入文件npt.mdp，现对里面的各种编辑项目做简单注释。
###npt.mdp###
title = Protein-ligand complex NPT equilibration define = -DPOSRES ; position restrain the protein and ligand ; 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 energygrps = Protein JZ4 ; Bond parameters continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; 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 tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_JZ4 Water_and_ions ; 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 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 refcoord_scaling = com ; 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 off after NVT
中文注释仅供参考
###npt.mdp###
title = Protein-ligand complex NPT equilibration # define = -DPOSRES ; #预处理控制拓扑文件 ; Run parameters integrator = md ; #指定积分算法，md:蛙跳牛顿积分算法，用于平衡动力学积分 nsteps = 50000 ; #积分或能量最小化步数 dt = 0.002 ; #积分步长 ; Output control nstxout = 500 ; #坐标保存到轨迹文件的频率 nstvout = 500 ; #速度保存到轨迹文件的频率 nstenergy = 500 ; #能量保存到轨迹文件的频率，必须是nstcalcenergy的倍数 nstlog = 500 ; # log文件更新频率 energygrps = Protein JZ4 #保存能量的组 ; Bond parameters continuation = yes ; #初试构象不约束，不复位，用于精确的继续计算或重计算 constraint_algorithm = lincs ; #约束算法 lincs ：不能用于角度约束 constraints = all-bonds ; #键约束，all-bonds:所有键约束 lincs_iter = 1 ; #迭代次数，用于LINCS约束精度，默认1 lincs_order = 4 ; #约束偶合矩阵阶次，用于LINCS约束精度，默认4 ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; #邻近列表搜索方法 nstlist = 10 ; #邻近列表更新频率 rcoulomb = 1.4 ; #短程库伦截断 rvdw = 1.4 ; #短程范德华力截断 ; Electrostatics coulombtype = PME ; #库伦计算方式 pme_order = 4 ; #PME插值，默认4表示3次插值 fourierspacing = 0.16 ; #FFT傅里叶变换格点间距，默认。。。，与PME同时使用 ; Temperature coupling tcoupl = V-rescale ; #指定热耦合方法 tc-grps = Protein_JZ4 Water_and_ions ; #热偶合组 tau_t = 0.1 0.1 ; #热偶合时间常数 ref_t = 300 300 ; #参考温度--恒温值，个数对应组 ; Pressure coupling pcoupl = Parrinello-Rahman ; #指定压力耦合方式 ；Parrinello-Rahman： pcoupltype = isotropic ; #isotropic:盒子各向同性 tau_p = 2.0 ; #压力耦合时间常数 ref_p = 1.0 ; #参考压力---恒压值，一般为1 bar compressibility = 4.5e-5 ; #水可压缩性，1 bar300K时为4.5e-5 bar-1 refcoord_scaling = com # ; Periodic boundary conditions pbc = xyz ; #周期性边界条件；xyz:使用周期性边界条件 ; Dispersion correction DispCorr = EnerPres ; #色散校正 ; Velocity generation gen_vel = no ; #速度生成；no:不生成速度。输入文件没有速度，则为0；
