[gmx-users] Applying a Uniform Shear

[David van der Spoel]

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.
>> 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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> 
> 
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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