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标题: 在NPT平衡时使用模拟退火缓慢升温，但是输出的温度没有升上去 [打印本页]

作者
Author: 霍元甲 时间: 2022-10-7 13:31
标题: 在NPT平衡时使用模拟退火缓慢升温，但是输出的温度没有升上去
各位老师同学大家好，

我想研究水溶液中的蛋白结构的稳定性，想后续看它在高温下（398K）解链的过程。我计划先npt，再放开位置限制进行生产动力学（md阶段）；
在npt平衡时使用模拟退火进行缓慢升温，虽然我在md阶段观察到了解链，但是我发现在npt输出的温度数据中，温度并没有升高，我很疑惑

这是我npt的文件

define    = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md       ; leap-frog integrator
nsteps    = 5000000    ; 2 * 50000 = 10 ns
dt       = 0.002    ; 2 fs
comm-mode       = Angular       ; remove center of mass translational and rotational velocity
; Output control
nstxout    = 10000    ; save coordinates every 1.0 ps
nstvout    = 10000    ; save velocities every 1.0 ps
nstenergy = 10000    ; save energies every 1.0 ps
nstlog    = 10000    ; update log file every 1.0 ps
; Bond parameters
continuation          = yes    ; Restarting after NVT
;constraint_algorithm = lincs    ; holonomic constraints
constraint_algorithm = SHAKE
constraints          = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter             = 1       ; accuracy of LINCS
lincs_order          = 4       ; also related to accuracy
; Neighborsearching
;rlist          = 0.8
cutoff-scheme = Verlet
ns_type       = grid    ; search neighboring grid cells
;nstlist       = 20       ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb       = 0.8    ; short-range electrostatic cutoff (in nm)
rvdw          = 0.8    ; short-range van der Waals cutoff (in nm)
; Electrostatics
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          ; modified Berendsen thermostat
tc-grps    = Protein  Non-Protein ; two coupling groups - more accurate
;tau_t    = 0.1    0.1          ; time constant, in ps
;ref_t    = 398    398          ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl             = Berendsen    ; Pressure coupling on in NPT
pcoupltype       = isotropic          ; uniform scaling of box vectors
tau_p             = 0.5                ; time constant, in ps
ref_p             = 1.013                ; reference pressure, in bar
compressibility    = 4.5e-5             ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
;Simulated annealing
annealing                      = single                               ;liner annealing
annealing-npoints       = 6                                              ;number of entries
annealing-time             = 0 1000000 1000000 1000000 1000000 1000000
annealing-temp             = 273 298 323 348 373 398
; Periodic boundary conditions
pbc    = xyz    ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
;gen_vel    = no       ; Velocity generation is off
gen_vel    = yes

作者
Author: 霍元甲 时间: 2022-10-7 13:37
不过我在md阶段的温度是平衡在398k的
这是我md的文件

; Run parameters
integrator  = md       ; leap-frog integrator
;nsteps    = 5000000000 ; 10us
nsteps    = 50000000 ; 100 ns
dt       = 0.002    ; 2 fs
comm-mode = Angular ; remove center of mass translational and rotational velocity
; Output control
;nstxout          = 0    ; save coordinates every 10.0 ps
nstxout          = 10000 ; save every 20.0 ps
nstvout          = 10000    ; save velocities every 10.0 ps
nstenergy          = 20000 ; save energies every 10.0 ps
nstlog             = 20000    ; update log file every 10.0 ps
nstxout-compressed  = 5000
compressed-x-precision =1000
compressed-x-grps = Protein
; Bond parameters
continuation          = yes    ; Restarting after NPT
constraint_algorithm = SHAKE    ; holonomic constraints
shake-tol = 0.0001 ; for shake algorithm
constraints          = H-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter             = 1       ; accuracy of LINCS
lincs_order          = 4       ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type       = grid    ; search neighboring grid cells
;nstlist       = 10       ; 20 fs, largely irrelevant with Verlet scheme
;nstlist       = 5
;rlist          = 0.8
;rlist          = 1.4
rcoulomb       = 0.8    ; short-range electrostatic cutoff (in nm)
vdwtype       = cutoff
rvdw          = 0.8    ; short-range van der Waals cutoff (in nm)
; Electrostatics
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          ; modified Berendsen thermostat
tc-grps    = Protein Non-Protein ; two coupling groups - more accurate
tau_t    = 0.1    0.1          ; time constant, in ps
ref_t    = 398    398          ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl             = Parrinello-Rahman    ; Pressure coupling on in NPT
pcoupltype       = isotropic          ; uniform scaling of box vectors
tau_p             = 0.5                ; time constant, in ps
ref_p             = 1.013                ; reference pressure, in bar
compressibility    = 4.5e-5             ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc    = xyz    ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel    = no       ; Velocity generation is off

作者
Author: Frozen-Penguin 时间: 2022-10-7 13:58
annealing-time 的单位好像是ps吧，模拟总时长比这几个时间短多了

作者
Author: 霍元甲 时间: 2022-10-8 11:00

Frozen-Penguin 发表于 2022-10-7 13:58
annealing-time 的单位好像是ps吧，模拟总时长比这几个时间短多了

啊！那我应该是当成步数了！感谢提示！！！！

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