toma0052 wrote:
Hello,
I am looking for a way in Gromacs that I could apply a uniform shear. I
have looked through the manual, and it seems that the methods for applying
shear are using the cos_acceleration option or the deform option. The deform
option may work for me. However, I was reading in Allen and Tildesley's book
about a method for applying a uniform shear which involves a modification to
the PBC (In fact, I think it is what's depicted on the book's cover).
Essentially, the simulation box is held fixed, and the boxes above move in
one direction (+x) and the boxes below move in the opposite direction (-x).
Is there any way that I can do something like this in Gromacs? I have
searched the mailing list as well, but have come up empty handed.
My system is a lipid bilayer in water. I would like to look at this
system's response to a shear force, but I am not interested in any viscosity
calculations, so I am not sure cos_acceleration would be helpful to me. If I
use deform, I am worried that at long times I will get a simulation box with
some very sharp angles. If the above procedure is not possible in Gromacs,
would it make sense to use the deform option in a sinusoidal fashion doing
several simulations where the box is first deformed one way and then deformed
back again in the opposite direction?
you can use normal accelerations (see mdp options)
Thank you,
Mike
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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