问:
因为opls_aa力场中有专门的离子液体的力场而选。用的lammps软件。在模拟中,问题好多,跑着跑着,原子就会missing。初始位置,分子间隔的挺远,大约10埃,我dump force后发现,力都好大,不清楚啥个原因。
打算换个力场试试,不知哪个力场好点。
答1:
是用Pauda他们组的力场吗?二面角只有三个参数v1,v2,v3。我现在是刚开始研究这个,这个问题已经困了我好几天了,一直没找出啥问题来。希望你花一点点时间看看我的输入文件吧。
LAMMPS input file
units real
boundary p p p
atom_style full #uncharged molecules, with bond, angle, dihedral, improper dihedral
bond_style harmonic
angle_style harmonic
dihedral_style opls
pair_style lj/cut/coul/long 12
pair_modify mix geometric tail yes
kspace_style ewald 1.0e-4
#read_restart restart.mix.*
read_data data.il
#read_restart restart.mix.*
#fix 1 all shake 0.0001 20 10 b 3
neighbor 2.0 bin
neigh_modify delay 3 every 1 check yes #delay 3
fix 2 all langevin 300.0 300.0 0.2 48279
fix 3 all nve (文献上说可以先布朗运动下,所以我也设置了了一下)
timestep 0.1
dump 1 all custom 20000 dump.atom.*.lammpstrj xu yu zu
dump 2 all custom 20000 dump.force.* id mol type element fx fy fz
dump_modify 1 flush yes
dump_modify 2 flush yes
thermo_style custom step temp press etotal vol lx ly lz
thermo 1000
thermo_modify flush yes
run 1000000
我是做的(mmpy)(tsfi)这个分子,就两对分子。我真的不知道哪里有问题。。。
答2:
我在nve系综下跑的minimize。我的参数是
minimize 1.0e-4 1.0e-6 100 1000
min_style hftn
min_modify dmax 0.2
我的结果是:(我从log里面拷出来的)
minimize 1.0e-4 1.0e-6 100 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Ewald initialization ...
G vector = 0.227629
vectors: actual 1d max = 2748 10 4630
Memory usage per processor = 24.4557 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 161.97025 59.620071 221.59032 -139.69835
52 0 139.99619 32.197295 172.19348 -13.155359
Loop time of 0.369925 on 48 procs for 52 steps with 72 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
221.590316114 172.205685403 172.193484683
Force two-norm initial, final = 334.999 8.36533
Force max component initial, final = 89.5407 2.13135
Final line search alpha, max atom move = 0.000551252 0.00117491
Iterations, force evaluations = 52 255
Pair time (%) = 0.000742118 (0.200613)
Bond time (%) = 0.000933076 (0.252234)
Kspce time (%) = 0.182548 (49.3473)
Neigh time (%) = 0 (0)
Comm time (%) = 0.176163 (47.6214)
Outpt time (%) = 0 (0)
Other time (%) = 0.00953816 (2.57841)
Nlocal: 1.5 ave 21 max 0 min
Histogram: 44 0 0 0 0 0 1 1 0 2
Nghost: 38.5625 ave 72 max 0 min
Histogram: 12 0 0 3 6 3 7 2 1 14
Neighs: 27.2708 ave 471 max 0 min
Histogram: 44 0 0 0 2 0 0 0 1 1
Total # of neighbors = 1309
Ave neighs/atom = 18.1806
Ave special neighs/atom = 10.2222
Neighbor list builds = 0
Dangerous builds = 0
min_style hftn
min_modify dmax 0.2