[gmx-users] under boundary to box size?

herbst at fhi-berlin.mpg.de herbst at fhi-berlin.mpg.de
Tue Aug 10 13:28:22 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, so that all water and the solute
molecule flie 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.
Is there an under boundary to the box size or is this a representation
problem in ngmx?
What can I do?


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