We want to simulate water transport through channel by osmotic
pressurce using Gromacs software. The force on the water molecules
is usually applied only in a buffer zone, not on all water
molecules. How to set up my system. In my opion, we can only define
a simple group by index. Water molecules are moving, so the water
molecules in a buffer zone change frequently. How to define the
group of water molecules in a buffer zone. Gromacs can do it?
thanks!
First: what is a 'buffer zone'? And why do you need one? Also, you
should be able to model osmotic pressure with the application of
special forces, no?
Perhaps I entirely missed the point. If not, here is what came to mind.
One admitedly strange way to apply forces based on position would be
to run gromacs in very short segments using the pull code to apply the
forces and every time you stop gromacs run your own scripts or gromacs
utilities to determine which waters should be feeling your force and
make a new .ndx file to cause that to happen in the next mrdun
segment. You should then determine how long to run your segments based
on the diffusion of normal water and take an average of how long it
before recalculating. I figure 0.4A^2/ps diffusion suggests segments
of < 10ps (but don't take my word for it) making this a very time
consuming endeavour.
Also not that this method would destroy dynamics information about the waters.
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