[gmx-users] Applying a Uniform Shear

toma0052 toma0052 at umn.edu
Thu Sep 13 19:00:12 CEST 2007


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?

Thank you,
Mike




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