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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
