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月牙_2012

新虫 (初入文坛)

应助: 1 (幼儿园)
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虫号: 2180256
注册: 2012-12-11
专业: 分离过程

[求助] 用lammps作PMF不平衡

各位大神，我尝试用LAMMPS中fix smd命令做PMF。体系是中间为石墨烯，是石墨烯左右两边是NaCl溶液。准备分别做钠离子、氯离子和水的PMF.但运行的结果，却是左右不对称。请各位大神帮我看看出现什么问题了。谢谢！！！
units real
atom_style full
neighbor 2.0 bin
boundary p p p
read_data H-PMF.data

#lj potentials
pair_style  lj/cut/coul/long 10.0
pair_coeff 1 1 0.07 3.55
pair_coeff 2 2 0.07 3.55
pair_coeff 3 3 0.03 2.42
pair_coeff 4 4 0.1553 3.166
pair_coeff 5 5 0 0
pair_coeff 6 6 0.1 2.583
pair_coeff 7 7 0.1 4.401
pair_coeff 8 8 0.1553 3.166
pair_coeff 9 9 0 0
pair_coeff 10 10 0.1 2.583
pair_coeff 11 11 0.1 4.401
pair_coeff 12 12 0.1553 3.166
pair_coeff 13 13 0 0

pair_modify mix arithmetic
#special_bonds charmm

bond_style harmonic
bond_coeff 1 469 1.40
bond_coeff 2 367 1.080
bond_coeff 3 450 1.0
bond_coeff 4 450 1.0

angle_style harmonic
angle_coeff 1 63 120
angle_coeff 2 35 120
angle_coeff 3 55 109.47
angle_coeff 4 55 109.47

#special_bonds lj/coul 0.0 0.0 0.5
neigh_modify delay 0 every 1 check yes

kspace_style pppm 1.0e-4

#kspace_modify slab 3.0

special_bonds  lj 0.0 0.0 0.5 coul 0.0 0.0 0.5

#define groups
group GHE type 1 2 3
group shui1 type 4 5 12 13
group shui2 type 8 9
group LJ type 6 7 10 11
group shui union shui1 shui2
group and union shui LJ
group smd-w type 12 13

neigh_modify exclude group GHE GHE
#neigh_modify exclude type 9 9
#neigh_modify delay 0 every 1

#minimize 1.0e-4 1.0e-6 100 1000

#velocity and create 298.0 4928459 units box
velocity GHE set 0.0 0.0 0.0 units box

fix 1 GHE setforce 0 0 0
fix 2 and nvt temp 298.0 298.0 100.0
fix 3 GHE rigid/nvt group 1 GHE temp 298.0 298.0 100.0 force * off off off torque * off off off
fix 4 smd-w rigid group 1 smd-w force * off off on torque * off off off
fix 5 shui shake 0.0001 20 0 b 3 4 a 3 4
fix 6 smd-w smd cvel 20 -0.000005 tether NULL NULL 15 0.0

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