Gromacs分段做NPT密度为什么呈现周期波动

lyl · 发表于 Post on 2021-3-7 11:01:04

请问，Gromacs做NPT分段压缩盒子时，每段密度是收敛的，但下一段开始密度又会发生变化，总体来看密度呈现周期波动，一直不收敛，这是什么原因，该如何解决

sobereva · 发表于 Post on 2021-3-7 23:47:44

说清楚什么体系、什么热浴、什么控压参数。“分段压缩盒子”语义不明
如果是PR压浴，尝试改成berendsen

lyl · 发表于 Post on 2021-3-8 15:28:27

本帖最后由 lyl 于 2021-3-8 15:38 编辑

带有CH2OH极性基团的五元环烃与乙烯交替共聚，为了使密度稳定，进行分段压缩。不带极性基团密度比较稳定，随着极性基团含量增加密度出现周期变化
mpirun -np 4 gmx_mpi mdrun -ntomp 6，使用了4块GPU
采用Berendsen热浴和Berendsen控压
mdp参数
title                   = POSS
integrator             = md
dt                      = 0.001
nsteps                = 100000
nstxout                = 10000
nstvout                =
nstlog                = 1000
nstenergy             = 1000
nstxout-compressed    = 10000  ; output for .xtc file
compressed-x-grps       = System
nstlist                = 10
ns_type                = grid
rlist                   = 1.0
coulombtype             = PME
rcoulomb                = 1.0
vdw_type                = Cut-off
cutoff-scheme          = Verlet
rvdw                   = 1.0
rvdw_switch             = 0
tcoupl                = Berendsen
;tcoupl                = nose-hoover
tc-grps                = system
tau_t                   = 0.5
ref_t                   = 800
Pcoupl                = Berendsen
Pcoupltype             = isotropic
tau_p                   = 5.0
compressibility       = 4.5e-5
ref_p                   = 1.0
gen_vel                = yes
gen_temp                = 1000
gen_seed                = 13029
constraint-algorithm    = SHAKE
constraints             = none
pbc                   = xyz
epsilon_rf             = 0
DispCorr                = EnerPres
fourierspacing          = 0.12

sobereva · 发表于 Post on 2021-3-16 08:07:37

tau_p太大了，设小再试

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[GROMACS] Gromacs分段做NPT密度为什么呈现周期波动