计算化学公社

标题: 求助：想用gromacs进行电解质的退火模拟，出现segmentation fault错误 [打印本页]

作者
Author: sowhat 时间: 2025-5-20 15:39
标题: 求助：想用gromacs进行电解质的退火模拟，出现segmentation fault错误
mdp文件如下，在执行命令grompp_mpi -f ann.mdp -c npt.gro -p topol.top -o ann.tpr 时出现segmentation fault错误。把annealing这几行删掉可以正常产生tpr文件，求大神指点

title             = NPT equilibration for system
;define             = -DPOSRES       ; position restrain the protein
; Run parameters
integrator       = md             ; leap-frog integrator
nsteps             = 20000000             ; 2 * 50000 = 100 ps
dt                   = 0.001             ; 2 fs
; Output control
nstxout             = 50000       ; save coordinates every 0.2 ps
nstvout             = 50000       ; save velocities every 0.2 ps
nstenergy       = 50000       ; save energies every 0.2 ps
nstlog             = 50000       ; update log file every 0.2 ps
nstxout-compressed          = 50000 ; save compressed coordinates every 10.0 ps
                              ; nstxout-compressed replaces nstxtcout
compressed-x-grps =    ; replaces xtc-grps
; Bond parameters
continuation       = yes                   ; first dynamics run
constraint_algorithm = lincs       ; holonomic constraints
constraints       = none    ; all bonds (even heavy atom-H bonds) constrained
lincs_iter       = 1                         ; accuracy of LINCS
lincs_order       = 4                         ; also related to accuracy
; Neighborsearching
ns_type             = grid             ; search neighboring grid cels
nstlist             = 10                   ; 10 fs
rlist             = 1.2             ; short-range neighborlist cutoff (in nm)
rcoulomb       = 1.2             ; short-range electrostatic cutoff (in nm)
rvdw             = 1.2             ; short-range van der Waals cutoff (in nm)
cutoff-scheme = Verlet
; 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             = TFO  AL       DXE; three coupling groups - more accurate
tau_t             = 0.2       0.2  0.2 ; time constant, in ps
ref_t             = 298  298 298 ; reference temperature, one for each group, in K

; Pressure coupling is off
pcoupl             = Parrinello-Rahman
pcoupltype  = isotropic
tau_p                      = 1.0                         ; time constant, in ps
ref_p                      = 1.0                   ; reference pressure, in bar
compressibility    = 4.5e-5
annealing = single  single  single
annealing-npoints= 0 0 4
annealing-time= 0  1000 2000  4000
annealing-temp= 298 349  400  400
; Periodic boundary conditions
pbc                   = xyz             ; 3-D PBC
; Dispersion correction
DispCorr       = EnerPres       ; account for cut-off vdW scheme
; Velocity generation
gen_vel             = no             ; assign velocities from Maxwell distribution
gen_temp       = 250             ; temperature for Maxwell distribution
gen_seed       = -1             ; generate a random seed
; COM motion removal

作者
Author: sobereva 时间: 2025-5-21 05:49
退火点没法写0个

没事甭写fourierspacing = 0.16 ，避免被以讹传讹

作者
Author: sowhat 时间: 2025-5-21 09:08

sobereva 发表于 2025-5-21 05:49
退火点没法写0个

没事甭写fourierspacing = 0.16 ，避免被以讹传讹

请问如果要给单个组退火要怎么写呢

作者
Author: sobereva 时间: 2025-5-22 03:56

sowhat 发表于 2025-5-21 09:08
请问如果要给单个组退火要怎么写呢

某个组温度若始终恒定，退火点至少也得写1；或者写2，前、后的参考温度设成相同的值

欢迎光临计算化学公社 (http://bbs.keinsci.com/)