GROMACS运行参数之nvt.mdp文件详解

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nvt平衡过程中需要用到输入文件nvt.mdp，现对里面的各种编辑项目做简单注释。

###nvt.mdp###

title       = Protein-ligand complex NVT equilibration define      = -DPOSRES  ; position restrain the protein and ligand; Run parametersintegrator  = md        ; leap-frog integratornsteps      = 50000     ; 2 * 50000 = 100 psdt          = 0.002     ; 2 fs; Output controlnstxout     = 500       ; save coordinates every 1.0 psnstvout     = 500       ; save velocities every 1.0 psnstenergy   = 500       ; save energies every 1.0 psnstlog      = 500       ; update log file every 1.0 psenergygrps  = Protein JZ4; Bond parameterscontinuation    = no            ; first dynamics runconstraint_algorithm = lincs    ; holonomic constraints constraints     = all-bonds     ; all bonds (even heavy atom-H bonds) constrainedlincs_iter      = 1             ; accuracy of LINCSlincs_order     = 4             ; also related to accuracy; Neighborsearchingcutoff-scheme   = Verletns_type         = grid      ; search neighboring grid cellsnstlist         = 10        ; 20 fs, largely irrelevant with Verletrcoulomb        = 1.4       ; short-range electrostatic cutoff (in nm)rvdw            = 1.4       ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype     = PME       ; Particle Mesh Ewald for long-range electrostaticspme_order       = 4         ; cubic interpolationfourierspacing  = 0.16      ; grid spacing for FFT; Temperature couplingtcoupl      = V-rescale                     ; modified Berendsen thermostattc-grps     = Protein_JZ4 Water_and_ions    ; two coupling groups - more accuratetau_t       = 0.1   0.1                     ; time constant, in psref_t       = 300   300                     ; reference temperature, one for each group, in K; Pressure couplingpcoupl      = no        ; no pressure coupling in NVT; Periodic boundary conditionspbc         = xyz       ; 3-D PBC; Dispersion correctionDispCorr    = EnerPres  ; account for cut-off vdW scheme; Velocity generationgen_vel     = yes       ; assign velocities from Maxwell distributiongen_temp    = 300       ; temperature for Maxwell distributiongen_seed    = -1        ; generate a random seed

中文注释仅供参考

###nvt.mdp###

title       = Protein-ligand complex NVT equilibration     #define      = -DPOSRES  ; #预处理控制拓扑文件; Run parametersintegrator  = 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 controlnstxout     = 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 parameterscontinuation    = no            ; # no：初试构象约束，并复位，第一次MDconstraint_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1lincs_order     = 4             ; #约束偶合矩阵阶次，用于LINCS约束精度，默认4; Neighborsearchingcutoff-scheme   = Verletns_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; Electrostaticscoulombtype     = 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 couplingtcoupl      = 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 couplingpcoupl      = no        ; #指定压力耦合方式；no:不耦合，即固定盒子大小; Periodic boundary conditionspbc         = xyz       ; #周期性边界条件；xyz:使用周期性边界条件; Dispersion correctionDispCorr    = EnerPres  ; #色散校正; Velocity generationgen_vel     = yes       ; #速度生成 ；yes：根据麦克斯韦速度分布函数生成速度，只对md有意义gen_temp    = 300       ; #体系温度，用于麦克斯韦速度分布gen_seed    = -1        ; #初始速度初试随机数，-1表示为进程的ID数

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