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标题: gromacs模拟蛋白结果异常，请教mdp参数设置 [打印本页]

作者
Author: Sagaf 时间: 2025-4-14 17:37
标题: gromacs模拟蛋白结果异常，请教mdp参数设置
各位好，我做了一个50ns的模拟，看rmsd应该是稳定了，但是抽了几帧结构发现跑拉丝了。麻烦各位老师帮忙看下是不是mdp文件设置不合理，谢谢！

title                = MD simulation
; Run parameters
integrator             = md       ; leap-frog integrator
nsteps                = 25000000 ; 2 * 25000000 = 50000 ps (50 ns)
dt                   = 0.002    ; 2 fs
; Output control
nstenergy             = 10000    ; save energies every 20.0 ps
nstlog                = 10000    ; update log file every 20.0 ps
nstxout-compressed    = 10000    ; save coordinates every 20.0 ps
nstvout                = 10000    ;
; Bond parameters
continuation          = yes    ; continuing from NPT
constraint_algorithm = lincs    ; holonomic constraints
constraints          = h-bonds ; bonds to H are constrained
lincs_iter             = 1       ; accuracy of LINCS
lincs_order          = 4       ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme          = Verlet
ns_type                = grid    ; search neighboring grid cells
nstlist                = 20       ; largely irrelevant with Verlet
rlist                = 1.2
vdwtype                = cutoff
vdw-modifier          = force-switch
rvdw-switch          = 1.0
rvdw                   = 1.2    ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype          = PME    ; Particle Mesh Ewald for long-range electrostatics
rcoulomb             = 1.2
pme_order             = 4       ; cubic interpolation
fourierspacing       = 0.12    ; grid spacing for FFT
; Temperature coupling
tcoupl                = Nose-Hoover
tc-grps                = Protein Non-Protein ; two coupling groups - more accurate
tau_t                = 1.0 1.0                   ; time constant, in ps
ref_t                = 300 300                   ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl                = Parrinello-Rahman          ; pressure coupling is on for NPT
pcoupltype             = isotropic                   ; uniform scaling of box vectors
tau_p                = 2.0                         ; time constant, in ps
ref_p                = 1.0                         ; reference pressure, in bar
compressibility       = 4.5e-5                      ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc                   = xyz    ; 3-D PBC
DispCorr             = EnerPres
; Velocity generation
gen_vel                = no       ; continuing from NPT equilibration

作者
Author: student0618 时间: 2025-4-14 21:36
用trjconv pbc -mol处理周期性边界。

作者
Author: Sagaf 时间: 2025-4-15 08:39

student0618 发表于 2025-4-14 21:36
用trjconv pbc -mol处理周期性边界。

好的，我试试

作者
Author: Sagaf 时间: 2025-4-15 09:23

student0618 发表于 2025-4-14 21:36
用trjconv pbc -mol处理周期性边界。

已解决，谢谢

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