[gmx-users] Applying a Uniform Shear

[toma0052]

Hello,
     Thanks for the rapid response, although I am not sure I completely
understand what you mean.  The accelerate option adds a constant acceleration
to whatever atoms I choose with acc_grps.  However, if I want a uniform
shear, I need to give atoms an acceleration dependent on their position
within the simulation box (z-coordinate in the case of my bilayer lying in
the x-y plane and the acceleration being in the x-direction).  I don't see
how I could do this with the accelerate mdp option.  Am I missing something
here?

Thanks,
Mike





On 13 Sep 2007, David van der Spoel wrote:
> 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
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