[gmx-users] where is water?

[Ragothaman Yennamalli]

Thanks...Glad to realize the newer version of gromacs makes life easier.
Raghu

On Mon, Jul 11, 2011 at 11:38 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Ragothaman Yennamalli wrote:
>
>> Hi Friends,
>>
>> When I run pdb2gmx, it automatically asks which water topology should be
>> included. Also, in the .top file the lines included are:
>>
>> ; Include water topology
>> #include "gromos53a6.ff/spc.itp"
>>
>> However, I do not see any water molecules in the .gro file. So, was water
>> included or not?
>>
>>
> pdb2gmx does not add water.  That's what genbox does.  The water selection
> utility in pdb2gmx is intended to make your life easier when it comes to
> solvation - the water topology is already present (#included in the .top).
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
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> ICTAS Doctoral Scholar
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> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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