14、支持acc_grps选项。空间电场(ElectricFields:不支持。混合量子力学与分子力学(QMMM:不支持。4.测试方法Gromacs从4.5版本开始支持GPU加速的分子动力学模拟,GPU部分的计算使用了斯坦福大学生物医学计算研究中心(SimbiosNIHCenterforBiomedicalComputationatStanford的OpenMM库的加速支持,Gromacs和OpenMM两个部分均是开源的。当...
46 把右边的分子定义为一个group，mdp里设置acc-grps为这个组，accelerate设置施加的加速度的矢量，等同...
tcoupl = V-rescale ; modified Berendsen thermostattc-grps = Protein Non-Protein ; 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 coupling is offpcoupl = no ; no pressure coupling ...
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucl...
该教程为使用 GROMACS 软件进行分子动力学模拟的一个入门教程,本次教程以「水中的溶菌酶」为例学习如何准备和运行一个典型的蛋白质在水中的分子动力学模拟。在OpenBayes 平台使用 NVIDIA RTX 4090 显卡配置的 GPU 版本的 GROMACS,经过 GPU 并行计算后的计算效率大大提高,速度可达到 255ns/day!以下是速度表现:...
order = 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature coupling is ontcoupl = V-rescale ; modified Berendsen thermostattc-grps = Protein Non-Protein ; two coupling groups - more accuratetau_t = 0.1 0.1 ; time constant,...
2，; Non-equilibrium MD stuff = acc-grps = Water accelerate =0.1 0.0 0.0 freezegrps...
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 ...
energygrps = CNT NTR ; NEIGHBORSEARCHING PARAMETERS cutoff-scheme = Group nstlist = 5 ...
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 ...