[gmx-developers] a problem about the implement of shear flow in gromacs

[Berk Hess]

Hi,

If you set an off-diagonal element in deform, you get shear flow.

Cheers,

Berk

On 10/04/2016 07:40 PM, J Hu wrote:
> Hi Berk,
>
> Thanks for your advice!
>
> However, I'm sorry that I do not really understand your point... The 
> deform md option should be turned off by default right? So how could I 
> adjust it to realize my implement of shear flow? Could you please tell 
> me some more details about that if you are available? Thanks!
>
> As for the patch, yes, I would really appreciate it if you could share 
> it with me!
>
> Best wishes
>
> Jin
>
> 2016-10-04 14:22 GMT+01:00 Berk Hess <hess at kth.se <mailto:hess at kth.se>>:
>
>     Hi,
>
>     I think the defrom MD option can do what you want.
>     It does not apply the proper SLLOD equations, but I think this
>     does not matter under most conditions. If you want to use SLLOD, I
>     have a patch for that.
>
>     Cheers,
>
>     Berk
>
>
>     On 10/04/2016 03:06 PM, J Hu wrote:
>>
>>     /Hello,/
>>
>>     /
>>     /
>>
>>     /I ///have recently /tried to simulate a shear flow in a
>>     molecular dynamics model by implementing the //Lees Edwards
>>     boundary (periodic shear flow) conditions in GROMACS. However the
>>     ///results /I got are strange ...
>>
>>     /
>>
>>     /I added the effect of the shear, delta_U(y)=gamma*dy, where
>>     gamma = dU/dy by modifying the coordinate equation dx/dt = ... +
>>     gamma*dy  in the x-direction so that coordinate change along the
>>     x direction becomes  x(t+dt) = x(t) + dt*[v(t) +gamma*dy]. The
>>     ///calculation of the molecular dynamics /velocity, v(t)  from
>>     the pair potential was kept the same as usual from Newton's
>>     second law without any change.
>>     /
>>
>>     /
>>     /
>>
>>     /To compare with the analytical shear flow solution U(y), I then
>>     wrote a routine that averages all atoms velocities in time as
>>     well as in the homogeneuous x&z directions and so obtained the
>>     velocity profile along the y-direction (the  velocity
>>     ///information /was directly obtained from the gro
>>     files). However, strangely, the resulting profile of the mean
>>     atom velocity, which I expected to be flat around zero, turned
>>     out to have a negative slope, -gamma, as if the model tried to
>>     compensate for the positive shear flow I was trying to impose.
>>     This effect is very consistent for a range of different shears --
>>     from moderate to very small gamma. So I thought this is due to
>>     the thermostat or some other intrinsic GROMACS feature which
>>     checks the atom velocities/deviations and //holds the velocities
>>     to correspond to the uniform state, hence, creates an
>>     "anti-shear" effect.
>>
>>     Did someone encounter a similar problem in GROMACS and know how
>>     to disable these stabilising  features of ///GROMACS/?
>>     Or, does someone know a simpler method how to generated a shear
>>     flow in GROMACS ?///
>>
>>     /
>>     /
>>
>>     /Thanks a lot./
>>
>>     /
>>     /
>>
>>     /Best wishes/
>>
>>     /
>>     /
>>
>>     /Jin/
>>
>>
>>
>
>
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