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标题: 求助：动力学报错，报错信息无法理解，且step文件如图 [打印本页]

作者
Author: 崔智勇 时间: 2021-6-24 18:38
标题: 求助：动力学报错，报错信息无法理解，且step文件如图
您好，蛋白配体复合物模拟的时候在mdrun的时候报错，提示的step如图，但是个人感觉和grompp环境的提示有关，其提示内容如下：
The bond in molecule-type IMP between atoms 3 O2P and 4 2HOP has an estimated oscillational period of 9.1e-03 ps, which is less than 5 times the time step of 2.0e-03 ps.
但是这里我不理解，9.1e-03 ps明明比2.0e-03 ps.要大，为什么还说小5倍呢？

另外，step文件在pymol里面已经散掉啦，但是在vmd里面是正常的（两个图都去掉水分子啦）
麻烦老师啦，祝您生活愉快

作者
Author: sobereva 时间: 2021-6-25 18:33
提示说的是9.1e-03 ps小于2.0e-03 ps的5倍（10e-03）

用2fs步长的时候记得应当用constraints = hbonds

有VMD还用pymol干嘛。有一个VMD就够了

作者
Author: 崔智勇 时间: 2021-6-26 18:49

sobereva 发表于 2021-6-25 18:33
提示说的是9.1e-03 ps小于2.0e-03 ps的5倍（10e-03）

用2fs步长的时候记得应当用constraints = hbonds

老师您好，我看了mdp文件，确实写了constraints=bonds
具体的mdp文件如下
title                = Protein-ligand complex MD simulation
; Run parameters
integrator             = md       ; leap-frog integrator
nsteps                = 50000000 ; 2 * 50000000 = 100000 ps (100 ns)
dt                   = 0.002    ; 2 fs
; Output control
nstenergy             = 5000    ; save energies every 10.0 ps
nstlog                = 5000    ; update log file every 10.0 ps
nstxout-compressed    = 5000    ; save coordinates every 10.0 ps
; 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       = 0.16    ; grid spacing for FFT
; Temperature coupling
tcoupl                = V-rescale                   ; modified Berendsen thermostat
tc-grps                = Protein_IMP Water_and_ions ; 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
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
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr             = no
; Velocity generation
gen_vel                = no       ; continuing from NPT equilibration

作者
Author: wmy1217 时间: 2023-5-10 16:44

崔智勇发表于 2021-6-26 18:49
老师您好，我看了mdp文件，确实写了constraints=bonds
具体的mdp文件如下
title = P ...

您好，我最近遇到了和您同样的问题，请问问题解决了吗，是怎么解决的呢

作者
Author: Huschein 时间: 2023-5-10 17:10
“constraints=bonds”看仔细一点，让你写constraints=hbonds

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