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

herbst at fhi-berlin.mpg.de herbst at fhi-berlin.mpg.de
Fri Aug 13 11:43:24 CEST 2004

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?


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