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标题: (已解决)gromacs退火后形成分立团簇 [打印本页]

作者
Author: 渡边京介 时间: 2023-11-8 19:22
标题: (已解决)gromacs退火后形成分立团簇
本帖最后由渡边京介于 2023-11-8 23:43 编辑

跑完NPT后压实了

————————————————————————————————————————————————————
两张图分别是退火前和退火后的样子，这种情况是不是初始盒子太大造成的呀

把两个盒子重叠之后可以发现团簇是在盒子的边界的，是否需要再mdp文件中定义一下什么条件？

integrator = md
dt       = 0.001 ;
nsteps    = 5000000 ;
comm-grps  = system
energygrps =
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog  = 500
nstenergy = 500
nstxout-compressed = 1000
compressed-x-grps  = system
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb    = 1.0
vdwtype    = cut-off
rvdw       = 1.0
DispCorr    = EnerPres
;
Tcoupl  = Berendsen
tau_t = 0.2
tc_grps = system
ref_t = 300
;
Pcoupl    = Berendsen
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
;
annealing = single
annealing_npoints = 11
annealing_time = 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000
annealing_temp = 0 500 300 500 300 500 300 500 300 500 300
constraints = h-bonds

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