[gmx-users] Inconsistent shifts

Mark Abraham mark.j.abraham at gmail.com
Tue Mar 8 17:40:58 CET 2016


I wouldn't worry about that warning from gmx traj. It's probably relevant
in some other context, but somebody wrote some dirty code that got re-used
in a context they did not intend.


On Tue, Mar 8, 2016 at 5:08 PM Jan Meyer <j.meyer at uni-wuppertal.de> wrote:

> Dear gmx users,
> i am using gmx 5.0.5 and i have a question concerning the error "There
> were x inconsistent shifts. Check your topology".
> I read some older posts about this error and do know that it comes together
> with something beeing wrong in the handling of pbc. I want to mention
> at the beginning
> that i have set "periodic-molecules = yes" in the mdp-file.
> My initial system consists of polyisoprene chains that contain up
> to 200 Monomer units. The system size is roughly 10x10x20 nm^3.
> It can be simulated (NPT) without any issues in parallel on 48 cores.
> Between the polymerchains i want to add sulfur bridges containing 2 sulfur
> atoms each. I am also able to stable run this system but when I use
> g_traj i get the above mentioned warning/error.
> I have also used the debug tool for g_traj to get more information.
> It said:
>         "Guessed pbc = xyz from the box matrix
>         mk_grey: shifts for atom 93303 due to atom 93302
>         are (1,2,0), should be (2,1,0)
>         dx = (-0.177,0.106,0.00900006)"
>  From the source code i tried to understand how these shifts are
> calculated.
> But so far i did not suceed. Is there maybe someone who can explain it
> in detail?
> I hope i could clearly explain my problem. If thats not the case and
> more information
> is needed please contact me.
> Thanks in advance
> Jan
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