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本帖最后由 anananante 于 2025-6-25 23:08 编辑
求助各位大佬,第一次做粗粒化,选用了martini力场,需要异氰酸酯和醇聚合。
我的键结参数都是martini官方教程中给出的bartender拟合生成的,pair coeffs遵循了martini3的粗粒化规则,目前就是单体盒子事先跑npt和nvt没有问题,一旦开始用fix bond/create指令成键,就会在运行一段时间后报错bond atom missing。我的体系按照数量最多能成2000个键,我调整过各种参数最多跑到成三四百个键左右就会报错。
请问是我的模型构建的有问题还是参数设置不合理?还是说martini有什么特殊的设置要求?下面贴上我的映射和in文件
目前是仅仅在令IPDI和PPG反应,OPPEA准备二阶反应,暂时还没用到,盒子中有这3个单体
# ----------------- Init Section -----------------
units real
dimension 3
boundary p p p
neighbor 3 bin
neigh_modify every 1 delay 0 check yes
#-----style-----------
atom_style full
pair_style lj/cut 20.0
pair_modify tail no
pair_modify mix arithmetic
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0 angle yes dihedral yes
# ----------------- Atom Definition Section -----------------
read_data stage1.data
# ============= coeffes Section ===================
pair_coeff 1 1 0.88191 4.7
pair_coeff 2 2 0.88191 4.7
pair_coeff 3 3 0.81021 4.7
pair_coeff 4 4 0.56165 4.1
pair_coeff 5 5 0.67876 4.1
pair_coeff 6 6 0.6214 4.1
pair_coeff 7 7 0.88191 4.7
pair_coeff 8 8 0.36089 3.4
pair_coeff 9 9 0.88191 4.7
pair_coeff 10 10 0.67876 4.1
# -- harmonic bondType parameter --
bond_coeff 1 7.3439 3.45
bond_coeff 2 7.3439 3.45
bond_coeff 3 7.3439 3.45
bond_coeff 4 7.3439 3.45
bond_coeff 5 7.3439 3.45
bond_coeff 6 7.3439 3.45
bond_coeff 7 7.3439 3.45
bond_coeff 8 7.3439 3.45
bond_coeff 9 7.3439 3.45
# -- cosine/squared angleType parameter --
angle_coeff 1 5.6804 180
angle_coeff 2 5.6804 180
angle_coeff 3 5.6804 180
angle_coeff 4 5.6804 180
angle_coeff 5 5.6804 180
angle_coeff 6 5.6804 180
angle_coeff 7 5.6804 180
angle_coeff 8 5.6804 180
# -- harmonic bondType parameter --
bond_coeff 10 62.9010 3.24
bond_coeff 11 111.7513 2.55
bond_coeff 12 4.6309 3.08
bond_coeff 13 85.6537 2.77
bond_coeff 14 125.9143 2.81
# -- cosine/squared angleType parameter --
angle_coeff 9 3.2886 125.4
angle_coeff 10 7.9372 115.28
angle_coeff 11 4.1634 119.19
angle_coeff 12 8.3339 109.88
# -- harmonic bondType parameter --
bond_coeff 15 6.6422 3.41
bond_coeff 16 4.5462 3.07
bond_coeff 17 282.3161 2.08
bond_coeff 18 294.4805 2.09
bond_coeff 19 33.2672 2.36
bond_coeff 20 296.0863 2.07
bond_coeff 21 269.0198 2.1
bond_coeff 22 273.3664 2.1
bond_coeff 23 292.1409 2.07
bond_coeff 24 7.0162 3.2
bond_coeff 25 7.0162 3.04
# -- cosine/squared angleType parameter --
angle_coeff 13 5.5137 125.26
angle_coeff 14 12.8128 103.29
angle_coeff 15 23.0826 92.45
angle_coeff 16 27.9845 145.31
angle_coeff 17 34.0288 106.72
angle_coeff 18 35.1402 163.08
angle_coeff 19 36.0842 161.65
angle_coeff 20 233.5891 104.79
angle_coeff 21 13.7640 180.0
angle_coeff 22 13.7640 180.0
#-----NVT(298K)--------------
#velocity all create 298 161013 rot yes dist gaussian
min_style sd
minimize 1.0e-4 1.0e-6 10000 1000000
timestep 1
fix stage1h all bond/create 200 1 5 4.2 24 prob 0.05 16101 iparam 1 9 jparam 1 10 #atype 21
dump mydump all custom 10000 stage1.lammpstrj id type x y z mol
fix 1 all nvt temp 298 298 100
restart 10000 tmp.restart
thermo_style custom step elapsed temp press pe ke etotal vol density f_stage1h[1] f_stage1h[2]
thermo 1000
run 10000000
write_data stage1out.data |
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