[gmx-users] under boundary to box size or ngmx-problem?

[herbst at fhi-berlin.mpg.de]

> herbst at fhi-berlin.mpg.de escreveu:
>
>> Hello all,
>>
>> I want to run a simulation for a small molecule in water. I need to
>> minimize the number of solvent molecules as far as possible in order to
>> keep simulation time reasonable. Here is my problem:
>> When I create a small box filled only with a few hundred water
>> molecules,
>> the box size in ngmx does not adapt to the calculation, so that all
>> water
>> and the solute molecule move apart in the ngmx-box and the solute has no
>> contact to water anymore. When I create a larger box with more than a
>> thousand water molecules, the box in ngmx is filled, but the simulation
>> takes too long. Can such a small box not be represented in ngmx
>> correctly
>> or is something wrong with the simulation?
>>
> I think there's no problem. You are watching a natural physical
> phenomenom,
> translational diffusion of your solute. If I understood correctly, you
> want
> to visualize the obtained trajectory, with your solute molecule within the
> box. Use trjconv -center -whole .... Check the manual help.

Hi Nuno,
using trjconv centers my solute molecule in the box, but the solvent still
moves out of my defined box, so it does not really help me. The problem is
that ngmx uses a larger box than I defined for the simulation. In the
beginning, all molecules are in the small box I defined. In fact I just
want to know whether in the gromacs simulation, the small box is used and
ngmx just does not display it right or whether I somehow defined the box
wrong and only a small part of it is filled with water?

> Best regards
> Nuno
>
>
>> Thanks,
>> Anna
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>>
>
>
>
> --
> -----------------------------------------------------
> Nuno Ricardo Santos Loureiro da Silva Ferreira
> Ph.D student
> Grupo de Química Biológica
> Departamento de Química
> Faculdade de Ciências e Tecnologia
> Universidade de Coimbra
> 3004-535 Coimbra
> Portugal
> www.biolchem.qui.uc.pt
> -----------------------------------------------------
> \" Do not worry about your dificulties in mathematics.
>    I can assure you that mine are still greater.\"
>                                        e=mc2
> -----------------------------------------------------
>
>
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