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

J Hu silvercece7 at gmail.com
Tue Oct 4 19:40:16 CEST 2016

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


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*
> --
> Gromacs Developers mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-developers_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20161004/4f303d3b/attachment.html>

More information about the gromacs.org_gmx-developers mailing list