[gmx-users] What do parameters in topology file mean ?

[大木啓輔]

Dear gmx users,

I have questions about topology file parameters.

I tried get topology files with topolbuild. But I was required to fix the *.top file
because H2O parameters were not given.

I could give some parameters in atoms and bonds, but I don't know some meanings of parameters.

topology file has some sections, for example atoms, bonds and angles etc..

I show the topology file below {

 [ bonds ]
;   ai  aj   funct      b0          kb
       1     2   1     0.10900      284512.       ;    C3-     H
       1     3   1     0.10900      284512.       ;    C3-     H
       :      :    :         :                 :
       6     7                                                 ;    HW-    OW
       :      :     :        :                 :

[ angles ]
; ai  aj  ak  funct      th0         cth
     3     1     2   1     107.800    276.1440     ;     H-    C3-     H
     4     1     2   1     107.800    276.1440     ;     H-    C3-     H
     :       :      :    :       :                :
    43   42   44                                              ;  HW- OW- HW-
     :       :      :                                                   

}

In bonds section, what do b0 and kb parameters mean?
I think respective they show distance of bond and energy of bond.

In angle section, what do th0 and cth mean?
Probably th0 means angle degree. But I cannot expect cth meaning.


Then, At the last of topology file {

; Include Position restraint file
; WARNING: Position restraints and distance restraints ought not be done together
#ifdef POSRES
#include "posreHYDRATE_4PT.itp"
#endif

; Include water topology
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

}

What do these mean? 
I think that ifdef POSRES is about restrain field.
And #include "spce.itp" means that SPC/E water model is exported to this topology file 
that has no parameters of water? So I have no need to give parameters to water?

Could you tell me solution to this problem, please?

Keisuke Ohki