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

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Hi,

Thanks!

Regards
Jin

> 在 2016年10月5日，08:05，Berk Hess <hess at kth.se> 写道：
> 
> 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>:
>>> 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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