toma0052 wrote:
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?
I see. In that case you'll have to do a tiny bit of programming. Check
src/mdlib/update.c
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.
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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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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