From: toma0052 <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: [gmx-users] Applying a Uniform Shear
Date: Thu, 13 Sep 2007 12:00:12 CDT
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?
I don't have Allen and Tildesley's at hand, but I guess all method should
be equivalent to or the deform option or the cos acceleration (or some
other periodic profile).
I think the deform option is what you want.
Your box angle will change, but that is exactly what happens in shear.
Note that when the angle exceeds 45 degrees it will jump to -45 degrees.
Berk.
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