[gmx-users] unusual trajectory

[Alex]

Group selection depends on what you want to see in the output 
trajectory. What I am trying to say is that per se nothing wrong seems 
to be happening -- you just have things crossing periodic boundaries.

The messages about inconsistent shifts could also mean atom shifts 
across boundaries, which is normal, though I don't recall ever seeing 
such messages from trjconv, and I work with solid structures under PBC 
and these messages always popup with other stuff, like gmx rdf, etc. At 
the same time, there _could_ of course be issues with your topology and 
your simulation. Noone can help with that, given this information.

Alex


On 7/22/2018 10:36 PM, Atila Petrosian wrote:
> Dear Alex,
>
> Which group I should select (system, CNT or lig)?
>
> After selecting each of them:
>
> There were 44 inconsistent shifts. Check your topology
>
> I'm confused.