[gmx-developers] a problem about the implement of shear flow in gromacs
Berk Hess
hess at kth.se
Tue Oct 4 15:22:01 CEST 2016
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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