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

[Berk Hess]

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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