[gmx-users] Frozen group moves!

[David van der Spoel]

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.

-- 
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