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

[Mark Abraham]

Hi,

I have no experience of topolbuild, but generally such tools won't
parametrize water for you because these are standardized. topolbuild likely
expects you to give it something that you might solvate in water later,
with the building blocks in e.g. the standard spce.itp.

Chapter 5 of the GROMACS reference manual is the resource to look at what
the various parameter quantities mean, but it is likely that you should not
be attempting to supply water parameters.

Mark

On Mon, Nov 28, 2016 at 6:22 AM 大木啓輔 <keisuke.ohki at keio.jp> wrote:

> 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
> --
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