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标题: Gromacs模拟离子液体退火时出现语法错误求助 [打印本页]

作者
Author: 小和尚 时间: 2019-12-22 10:52
标题: Gromacs模拟离子液体退火时出现语法错误求助
请问sob老师和给我老师朋友，我在模拟离子液体做退火处理时，出现以下错误：

Fatal error:
First time point for annealing > init_t.

加入tini_t = 0，在退火时间改为annealing-time = 0 1500 3000 4000 5000后还是不能解决。具体的mdp文件内容如下，请问大家应该如何解决呢？非常感谢您的解答。

title    = NPT equilibration
; Run parameters
integrator  = md       ; leap-frog integrator
nsteps    = 2500    ; 2 * 2500 = 5000 ps
dt       = 0.002    ; 2 fs
; Output control
nstxout    = 25000    ; save coordinates every 5.0 ps
nstvout    = 25000    ; save velocities every 5.0 ps
nstenergy = 25000    ; save energies every 5.0 ps
nstlog    = 25000    ; update log file every 5.0 ps
; Bond parameters
continuation = no    ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
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
rcoulomb       = 1.0    ; short-range electrostatic cutoff (in nm)
rvdw          = 1.0    ; 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
tcoupl    =  V-rescale                ; thermostat
tc-grps    = system ; two coupling groups - more accurate
tau_t    = 0.4  ; time constant, in ps
ref_t    = 473       ; 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
refcoord_scaling = com
;Simulated annealing
annealing             = single
annealing-npoints    = 4
annealing-time       = 1500 3000 4000 5000
init_t
annealing-temp       = 473 443 403 373
; 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 off after NVT

作者
Author: wbn 时间: 2019-12-22 14:11
annealing-time  里数字从0开始，数字数量要与annealing-npoints 相等
示例：
annealing          =  single
annealing-npoints =  5
annealing-time    =  0 500 1500 7500 8000
annealing-temp    =  298 598 598 298 298

作者
Author: sobereva 时间: 2019-12-22 16:00
标题里不要在末尾用叹号，给你改了
写tinit=0没有意义，本来默认就是0。annealing-time需要从0时刻开始指定（或者指定了tinit的时候，从tinit开始指定），要不然程序不知道一开始温度怎么控

作者
Author: 小和尚 时间: 2019-12-23 08:46

wbn 发表于 2019-12-22 14:11
annealing-time 里数字从0开始，数字数量要与annealing-npoints 相等
示例：
annealing = si ...

非常感谢！使用您给出的方法解决了问题。

作者
Author: 小和尚 时间: 2019-12-23 08:47

sobereva 发表于 2019-12-22 16:00
标题里不要在末尾用叹号，给你改了
写tinit=0没有意义，本来默认就是0。annealing-time需要从0时刻开始指 ...

非常感谢，根据您给的提示，把问题解决了。

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