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

Nuno R. L. Ferreira nunolf at ci.uc.pt
Fri Aug 13 16:00:48 CEST 2004

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.

Best regards

> 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
\" Do not worry about your dificulties in mathematics.
   I can assure you that mine are still greater.\"

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