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

[大木啓輔]

Hi Mr.Mark


Thank you for replying to my question.

I had thought that object molecules should have been separated from solvate water molecules,
because I intended to make hydrate structure.

As you tell me, at the last section in topology file,

; Include water topology
#include "spce.itp"

this description exists. 

So spce.itp file gives SPC/E model parameters to the topology file that lacks ones on H2O,
even if H2O molecules is not ones for solvation but object ones?

I was not sure of work of this description completely, but I'll try it and examine that.

Sincerely.


Keisuke Ohki
 
> 2016/11/28 22:23、Mark Abraham <mark.j.abraham at gmail.com>のメール:
> 
> 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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