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各位老师好,我最近使用GROMACS与cp2k连用做QM/MM分子动力学模拟发现total energy图像总突变,想问问各位老师这种情况正常吗?不正常的话可能的原因是什么。
.mdp文件如下
integrator = md ; leap-frog integrator
nsteps = 100000
dt = 0.001 ; 1 fs
; Output control
nstxout = 0 ; save coordinates
nstxout-compressed = 1
nstvout = 0 ; save velocities
nstenergy = 1 ; save energies
nstlog = 1 ; update log file
; Bond parameters
continuation = yes
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
; vdW
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
vdw-modifier = Potential-shift-Verlet
DispCorr = EnerPres
; Electrostatics
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; stochastic Bussi thermostat
tc-grps = System
tau_t = 1.0 ; value of tau (ps)
ref_t = 298 ; temperature (K)
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
; CP2K QMMM parameters
qmmm-cp2k-active = true ; Activate QMMM MdModule
qmmm-cp2k-qmgroup = QMatoms ; Index group of QM atoms
qmmm-cp2k-qmmethod = PBE ; Method to use
qmmm-cp2k-qmcharge = -1 ; Charge of QM system
qmmm-cp2k-qmmultiplicity = 1 ; Multiplicity of QM system
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