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标题: 求助：MD生产时报错No molecules were defined in the system [打印本页]

作者
Author: 学不会太难啦 时间: 2025-11-16 00:44
标题: 求助：MD生产时报错No molecules were defined in the system
本帖最后由学不会太难啦于 2025-11-16 01:01 编辑

我已经成功的进行了NPT平衡，并且也检查过了topol.top与NPT.gro的原子数目和顺序都是完全相同的，但是在MD生产的时候仍然出现这个错误，请问各位老师应该怎么解决呢？

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作者
Author: student0618 时间: 2025-11-16 01:57
1. 报错也放正文才容易阅读
2. 用什么指令grompp等完全没提，无法猜测。

作者
Author: 学不会太难啦 时间: 2025-11-16 08:11

student0618 发表于 2025-11-16 01:57
1. 报错也放正文才容易阅读
2. 用什么指令grompp等完全没提，无法猜测。

不好意思，我下次提问的时候会更清晰。
这是我用的指令和MD.mdp的内容，麻烦老师帮我看看有什么问题，非常感谢！
gmx grompp -f MD.mdp -c NPT.gro -t NPT.cpt -p topol.top -n index.ndx -maxwarn 2 -o MD.tpr

MD.mdp：
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_LIG 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

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