计算化学公社

标题: 求助gromcacs氢键寿命值太高 [打印本页]

作者
Author: zhaoqian 时间: 2022-6-27 09:17
标题: 求助gromcacs氢键寿命值太高
我计算的两个体系是乙二醇与水的溶液以及1，2-丙二醇与水的溶液，两个体系的计算参数都是一样的，可是算出来乙二醇的氢键寿命就比较正常13ps，其他文献也差不多是这个数，而1，2-丙二醇算出来的氢键寿命则为29ps，我就觉得很奇怪，我是先能量最小化到F<100，然后npt20ns（10ps输出一步），nvt20ns（10ps输出一步）（我看文献是先npt再nvt），接着md跑30ns（4ps输出一步），再用hbond -life 分析寿命的，按道理这两个体系的氢键寿命应该是差不多的吧，仔细对比了模拟参数，二者的模拟参数是一样的，可否拜托老师帮忙解答一下，万分感谢~

md 参数：
integrator             = md

dt                   = 0.002
nsteps                = 15000000
nstxout-compressed    = 2000
;nstxtcout             = 2000
nstcalcenergy          = 200
nstenergy             = 2000
nstlog                = 2000

cutoff-scheme          = Verlet
nstlist                = 20
rlist                = 1.0
vdwtype                = Cut-off
rvdw                   = 1.0
coulombtype          = pme
rcoulomb             = 1.0

tcoupl                = v-rescale  ;Nose-Hoover
tc_grps                = System
tau_t                = 1.0
ref_t                = 298.15

constraints          = h-bonds
constraint_algorithm = LINCS

gen-vel                = no
gen-temp             = 298.15
gen-seed             = -1

nstcomm                = 100
comm_mode             = linear
comm_grps             = System

pbc                   = xyz

npt参数：
integrator             = md
dt                      = 0.002    ;
nsteps                = 10000000  ;

;;Output parameters
nstxout                   = 50000             ;
nstvout                   = 50000             ;
nstenergy             = 5000          ;
nstlog                = 5000          ;
;nstxout-compressed    = 5000

continuation          = yes
constraint-algorithm    = lincs
constraints             = h-bonds

cutoff-scheme          = Verlet
ns_type                   = grid             ;
nstlist                   = 10          ;

coulombtype             = PME
rcoulomb                = 1.0

vdwtype                = Cut-off
rvdw                   = 1.0
DispCorr                = EnerPres

tcoupl                = V-rescale
tc-grps                = system
tau-t                   = 0.1
ref-t                   = 298.15
nhchainlength          = 1

pcoupl                = Parrinello-Rahman
tau_p                   = 1.0
compressibility       = 4.46e-5
ref_p                   = 1.0

; Periodic boundary conditions
pbc             = xyz             ;

; Velocity generation
gen_vel             = no             ;

nvt参数：
integrator             = md
dt                      = 0.002    ; 2.0 fs
nsteps                = 10000000  ;

;;Output parameters; save coordinates every 2.0 ps
nstvout                   = 100000
nstxout                   = 100000
nstenergy             = 10000
nstlog                = 10000
;nstxout-compressed    = 10000

continuation          = yes
constraint-algorithm    = lincs
constraints             = h-bonds

cutoff-scheme          = Verlet
ns_type                   = grid
nstlist                   = 10

coulombtype             = PME
rcoulomb                = 1.0
pme_order             = 4
fourierspacing       = 0.16

vdwtype                = Cut-off
rvdw                   = 1.0
DispCorr                = EnerPres

tcoupl                = V-rescale
tc-grps                = system
tau-t                   = 0.1
ref-t                   = 298.15
nhchainlength          = 1

pcoupl                = no

; Periodic boundary conditions
pbc             = xyz

; Velocity generation
gen_vel             = no

作者
Author: sobereva 时间: 2022-6-27 21:38
做一次NPT就够了，分三个任务完全多余

mdp没明显问题

乙二醇和1，2-丙二醇本来氢键寿命就可能明显不同，和与水的相互作用方式有关，可以做更细节的分析，诸如分析aNCI、sdf图，或者提取一些簇用量子化学研究等

作者
Author: zhaoqian 时间: 2022-6-28 11:00

sobereva 发表于 2022-6-27 21:38
做一次NPT就够了，分三个任务完全多余

mdp没明显问题

谢谢sob老师~

欢迎光临计算化学公社 (http://bbs.keinsci.com/)