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...
2，; Non-equilibrium MD stuff = acc-grps = Water accelerate =0.1 0.0 0.0 freezegrps...
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
tc-grps = Protein Non-Protein ; 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 is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT ...
compressed-x-grps = System ; save the whole system; Bond parameterscontinuation = yes ; Restarting after NPTconstraint_algorithm = lincs ; holonomic constraintsconstraints = h-bonds ; bonds involving H are constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy...
energygrps = CNT NTR ; NEIGHBORSEARCHING PARAMETERS cutoff-scheme = Group nstlist = 5 ...
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 = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodi...
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 ...
comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-...