计算化学公社

标题: gromacs体系小的时候没问题，体系增大就出现段错误 [打印本页]

作者
Author: Sunca 时间: 2024-6-26 22:18
标题: gromacs体系小的时候没问题，体系增大就出现段错误
本帖最后由 Sunca 于 2024-6-27 13:09 编辑

我用charmm-gui建模得到pdb文件，用pdb2gmx得到top文件，然后建盒子、能量最小化、nvt控温、npt控压，最后正式模拟。24个糖环的体系模拟顺利跑完没有问题，72个糖环的体系前面都没问题，但是正式模拟几百步就段错误。
(, 下载次数 Times of downloads: 14)

我检查了坐标和top文件没发现问题，下面是我的mdp参数，希望大家帮我看看有没有问题
1.能量最小化

define = -DFLEXIBLE
integrator = cg
nsteps  = 10000
emtol = 100.0
emstep = 0.01
;
nstxout = 100
nstlog = 50
nstenergy = 50
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
DispCorr = EnerPres
;
constraints = none
2.nvt控温
define = -DPOSRES
integrator = md
nsteps = 50000
dt = 0.002
nstxout = 500
nstvout  = 500
nstenergy = 500
nstlog = 500
continuation  = no
constraint_algorithm = lincs
constraints = h-bonds
lincs_iter  = 1
lincs_order = 4
cutoff-scheme = Verlet
ns_type = grid
nstlist = 10
rcoulomb = 1.0
rvdw = 1.0
DispCorr = EnerPres
coulombtype = PME
pme_order  = 4
fourierspacing = 0.16
tcoupl = V-rescale
tc-grps = Other  SOL
tau_t  = 0.1    0.1
ref_t  = 298    298
pcoupl = no
pbc  = xyz
gen_vel  = yes
gen_temp  = 300
gen_seed  = -1
3.npt控压
define  = -DPOSRES
integrator  = md
nsteps = 50000
dt = 0.002
nstxout = 500
nstvout = 500
nstenergy = 500
nstlog  = 500
continuation  = yes
constraint_algorithm  = lincs
constraints = h-bonds
lincs_iter  = 1
lincs_order  = 4
cutoff-scheme = Verlet
ns_type = grid
nstlist  = 10
rcoulomb  = 1.0
rvdw = 1.0
DispCorr  = EnerPres
coulombtype = PME
pme_order  = 4
fourierspacing = 0.16
tcoupl = V-rescale
tc-grps = Other SOL
tau_t = 0.1    0.1
ref_t  = 298    298
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
refcoord_scaling  = com
pbc  = xyz
gen_vel  = no
4.正式npt模拟
integrator = md
nsteps  = 100000000
dt = 0.001
nstxout  = 0
nstvout  = 0
nstfout = 0
nstenergy = 5000
nstlog  = 5000
nstxout-compressed = 5000
compressed-x-grps = System
continuation  = yes
constraint_algorithm  = lincs
constraints = h-bonds
lincs_iter = 1
lincs_order  = 4
cutoff-scheme  = Verlet
ns_type  = grid
nstlist  = 10
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
pme_order  = 4
fourierspacing = 0.16
tcoupl  = V-rescale
tc-grps  = Other SOL
tau_t = 0.1    0.1
ref_t = 300    300
pcoupl = Parrinello-Rahman
pcoupltype  = isotropic
tau_p  = 2.0
ref_p = 1.0
compressibility = 4.5e-5
pbc  = xyz
DispCorr  = EnerPres
gen_vel  = no

欢迎光临计算化学公社 (http://bbs.keinsci.com/)