石墨电极NaCl中固定石墨后，石墨没固定，水分子跑到石墨的位置固定

legend · 发表于 Post on 2023-12-27 11:07:25

石墨是用vmd建的，溶液用packmol建立，然后合并的
步长1fs时无法计算，命令是：
gmx grompp -f grompp.mdp -p topol.top -c start.gro -o run -maxwarn 2
gmx mdrun -s run -deffnm run -v -ntmpi 1 -ntomp 1
减小步长运行后
Steepest Descents:
Tolerance (Fmax) =  1.00000e+03
Number of steps =       50000
Step= 0, Dmax= 1.0e-02 nm, Epot=  1.47891e+10 Fmax= 1.60634e+10, atom= 4702
Step= 1, Dmax= 1.0e-02 nm, Epot=  6.29508e+09 Fmax= 3.20802e+09, atom= 4753
Step= 2, Dmax= 1.2e-02 nm, Epot=  4.42243e+09 Fmax= 5.80709e+08, atom= 4702
Step= 3, Dmax= 1.4e-02 nm, Epot=  4.05446e+09 Fmax= 9.59628e+07, atom= 4753
Step= 4, Dmax= 1.7e-02 nm, Epot=  3.98324e+09 Fmax= 1.45190e+07, atom= 4702
Step= 5, Dmax= 2.1e-02 nm, Epot=  3.96093e+09 Fmax= 2.27014e+06, atom= 4672
Step= 6, Dmax= 2.5e-02 nm, Epot=  3.95425e+09 Fmax= 1.53719e+06, atom= 4654
Step= 7, Dmax= 3.0e-02 nm, Epot=  3.95232e+09 Fmax= 1.31656e+06, atom= 4672
Step= 8, Dmax= 3.6e-02 nm, Epot=  3.95153e+09 Fmax= 1.73979e+06, atom= 4654
Step= 9, Dmax= 4.3e-02 nm, Epot=  3.95111e+09 Fmax= 4.35151e+05, atom= 4654
Step= 10, Dmax= 5.2e-02 nm, Epot=  3.95007e+09 Fmax= 2.31089e+06, atom= 4654
Step= 11, Dmax= 6.2e-02 nm, Epot=  3.94996e+09 Fmax= 1.15852e+05, atom= 4656
Step= 12, Dmax= 7.4e-02 nm, Epot=  3.94923e+09 Fmax= 2.71916e+05, atom= 4654
Step= 13, Dmax= 8.9e-02 nm, Epot=  3.94916e+09 Fmax= 7.24206e+04, atom= 4654
Step= 14, Dmax= 1.1e-01 nm, Epot=  3.94904e+09 Fmax= 1.25194e+05, atom= 4654
Step= 15, Dmax= 1.3e-01 nm, Epot=  3.94900e+09 Fmax= 1.04859e+04, atom= 4757

step 16: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step= 16, Dmax= 1.5e-01 nm, Epot=       inf Fmax= 1.25194e+05, atom= 4654
step 17: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

能量最小化时无法计算
同时想问一下：恒电荷法模拟是不是就是把上下电极表面的那层单独分配电荷

graphene.itp (444 Bytes, 下载次数 Times of downloads: 5)

grompp.mdp (1.73 KB, 下载次数 Times of downloads: 3)

start.gro (306.31 KB, 下载次数 Times of downloads: 2)

topol.top (200 Bytes, 下载次数 Times of downloads: 4)

legend · 发表于 Post on 2023-12-27 15:41:37

已解决

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[GROMACS] 石墨电极NaCl中固定石墨后，石墨没固定，水分子跑到石墨的位置固定

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