[gmx-users] Frozen group moves!

[Alex]

Hi,
Thanks for the response.

On Tue, Oct 22, 2019 at 02:04 David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> Den 2019-10-21 kl. 21:24, skrev Alex:
> > Dear all,
> > I freeze a group in my system in all directions as normal:
> > freezegrps               = GR
> > freezedim                = Y Y Y
> > So, I was expecting that the coordinates and velocities do not get
> updated
> > during the simulation, however, here is just part of in.gro and out.gro
> in
> > which the coordinates and velocity components have changed.
> >      #Y          #Z       #Vx     #Vy       #Vz
> >    #Y          #Z       #Vx     #Vy       #Vz
> >    0.271   0.049  0.0000  0.0000  0.0000                        |  0.271
> >   0.050  0.0000  0.0000 -0.0637
> >    0.249   0.020  0.0000  0.0000  0.0000                        |  0.249
> >   0.020  0.0000  0.0000  0.1823
> >    0.251   0.490  0.0000  0.0000  0.0000                        |  0.251
> >   0.490  0.0000  0.0000 -0.6805
> >    0.228   0.524  0.0000  0.0000  0.0000                        |  0.228
> >   0.524  0.0000  0.0000 -0.1568
> >    0.251   0.055  0.0000  0.0000  0.0000                        |  0.251
> >   0.055  0.0000  0.0000 -0.4114
> >    0.369  17.054  0.0000  0.0000  0.0000                        |  0.369
> > 17.055  0.0000  0.0000 -0.5276
> >    0.390   0.272  0.0000  0.0000  0.0000                        |  0.390
> >   0.273  0.0000  0.0000 -0.2386
> >    0.184   0.444  0.0000  0.0000  0.0000                        |  0.184
> >   0.444  0.0000  0.0000 -0.1694
> >    0.365   0.444  0.0000  0.0000  0.0000                        |  0.365
> >   0.444  0.0000  0.0000  0.1299
> >    0.361   0.553  0.0000  0.0000  0.0000                        |  0.361
> >   0.554  0.0000  0.0000 -0.5277
> >
> > Anybody knows what might be the reason and how one can avoid that to
> happen?
> >
> > Regards,
> > Alex
> >
> Do you have pressure coupling turned on?
> Alternatively, are the frozen coordinates part of a compound that is
> constrained?
> Both of these could cause this.

No, the simulation is in NVT ensemble by which I am trying to heat up the
system from room temperature to 443 K. However before heating, the system
had been equlibrated for 1 ns NVT and 2 ns NPT (1ns berendsen and 1 ns
parrinello rahman) by semi-isotropic. In equilibration everything was fine.

No it isn’t, the frozen group is not constrained.

Regards,
Alrx

>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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