SPC/E--在网上找到，随手保存备份

在网上找到，随手保存备用。

#water molecule.SPC/E model.

 

3 atoms ##分子模版中的原子总数
2 bonds ##模版中的bond总数
1 angles ##分子膜版中的总数

 

Coords
#原子ID X Y Z
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678

 

Types
#原子ID type
1 1
2 2
3 2

 

Charges
#原子ID charge
1 -0.8472
2 0.4236
3 0.4326

 

Bonds
#ID type atom1 atom2
1 1 1 2
2 1 1 3

 

Angles
#ID type atom1 atom2 atom3
1 1 2 1 3

 

Shake Flags
#ID flag ##0:不属于fix shake 作用的
1 1 ##1:shake two bonds and the angle they form
2 1 ##2:2-atom SHAKE cluster with a single bond
3 1 ##3:3-atom SHAKE cluster with two bonds
  ##4:4-atom SHAKE cluster with three bonds

Shake Atoms
#ID a b c ##flag=0 没有abc,忽略
1 1 2 3 ##flag=1 ID a(中心原子ID) b c
2 1 2 3 ##flag=2 ID a (ID of atom in bond with the lowest ID) b(ID of atom in bond with the highest ID)
3 1 2 3 ##flag=3 ID a(中心原子ID) b,c(IDs of other two atoms bonded to the central atom)
    ##flag=4 ID a(中心原子ID) b,c,d(IDs of other three atoms bonded to the central atom)

Shake Bond Types
#ID a b c ##flag=0 没有abc,忽略
1 1 1 1 ##flag=1 a(bondtype of the bond between the central atom and the first non-central atom) b(bondtype of the bond between the central atom and the 2nd non-central atom) c(the angle type of the angle between the 3 atoms)
2 1 1 1 ##flag=2 a(bondtype of the bond between the 2 atoms in the cluster)
3 1 1 1 ##flag=3 a(bondtype of the bond between the central atom and the first non-central atom) b(bondtype of the bond between the central atom and the 2nd non-central atom)
    ##flag=4 a(bondtype of the bond between the central atom and the first non-central atom) b(bondtype of the bond between the central atom and the 2nd non-central atom) c(bondtype of the bond between the central atom and the 3rd
non-central atom)

 

Special Bond Counts
#ID 1-2原子紧邻 1-3 1-4
1 2 0 0 ## 对于atom1 也就是o来说
2 1 1 0
3 1 1 0

 

##
##          atom1  
##               o
##               / \
##  atom2 h   h atom3
##
##  atom1 atom2就是1-2紧邻，atom1 atom3同理；--> 两个相邻原子间隔了1个键
##  atom2和atom3呢？三个原子间隔了2个键
## 显然 1-2原子紧邻 2个 ，1-3，1个，1-4，0个

 

Special Bonds

1 2 3  ###  ID 1-2紧邻 1-3
2 1 3  ###   1 2      3 #原子atom1 1-2紧邻的是原子2；1-3紧邻的是原子3
3 1 2  ###   2 1      3