[gmx-users] solvate with an exact number of solvent molecules

[David van der Spoel]

On 2015-03-02 22:25, Rebeca García Fandiño wrote:
> Thanks a lot for the suggestion, Jennifer.
> However, using gmx insert-molecules you cannot use the equilibrated solvent box, is it OK? I assume "your_insert.gro" should be a single molecule of solvent, right? I have tried using the whole box, and it does not work.
>
Maybe you need to look into gmx solvate?
> Best wishes,
>
> Rebeca.
>
> Dr. Rebeca Garcia
> Santiago de Compostela University
> Spain
>
> Hi Rebeca,
> In GROMACS 5.0,  I use
> gmx insert-molecules -f your.gro  -ci  your_insert.gro -o output.gro -nmol
> xxx
> where xxx is the number you want.
> Hope it helps.
> Jennifer
>
> On Mon, Mar 2, 2015 at 6:44 PM, Rebeca García Fandiño <regafan at hotmail.com>
> wrote:
>
>> Dear GROMACS users,
>> I am trying to do a systematic study using GROMACS and I would like to
>> have the same number of solvent molecules in all my systems. Using gmx
>> solvate in GROMACS 5.0 it is only possible to select the maximum number of
>> molecules in the box, but not a concrete number.
>> Does anyone knows about any way to solvate a molecule selecting an exact
>> number of solvent molecules in the box?
>> Thanks a lot in advance.
>> Best wishes,
>> Rebeca.
>>
>> Dr. Rebeca Garcia
>> Santiago de Compostela University
>> Spain
>>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se