[gmx-users] create a sphere of water molecules

[Esteban Gabriel Vega Hissi]

Hi,

You can try "packmol" (
http://www.ime.unicamp.br/~martinez/packmol/download.html) to create any
starting configuration of your interest. I found it very useful for random
initial configurations.

Hope this help.


Esteban Gabriel Vega Hissi
Área de Química Física
Departamento de Química
Universidad Nacional de San Luis
Argentina

On Wed, Apr 13, 2011 at 10:48 AM, Erik Marklund <erikm at xray.bmc.uu.se>wrote:

> Olga Ivchenko skrev 2011-04-13 15.20:
>
>
>>
>> Dear Gromacs Users,
>>
>> I want to add a sphere of water molecules around a ligand. I know I need
>> to use -shell option in genbox. But first I I need to create a sphere.
>> Please could you guide me?
>>
>> best,
>> Olga
>>
> Just fill the box with water, then run trjorder to sort the solvent
> according to their distance to the ligand. Having done that, you can just
> edit away the bottom part of the sorted gro-file to have your ligand in a
> ball of water.
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
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> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
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