[gmx-users] simulation of flow in channel
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 15 17:20:36 CET 2001
On Thu, 15 Nov 2001, Rui Qiao wrote:
> I am wondering if it is possible to use Gromacs to simulate the
>flow in a nano-channel.
> The perticular thing in this application is that periodic boundary
>condition is not allowed in channel height direction (z-direction). So I
>need to remove periodicity in z-direction.
> Is this possible?
Yes I think you can do it. It depends on how you want to model the walls.
If you have an e.g. nanotube with some solvent in it, the tube itself will
prevent the solvent fom going out. You just use a cut-off and enough
vacuum around the tube, and then apply normal 3D periodic boundary
If you want to do non equilibrium MD, you can turn on accelarations on the
solvent and wall in opposite directions (which yields a net flow
difference between wall and solvent which is the sum of the combined group
velocities). Interesting stuff.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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