[gmx-users] Inconsistent shifts

[Jan Meyer]

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