[gmx-users] Applying a Uniform Shear

[David van der Spoel]

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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se