[gmx-users] Fatal error:box vectors shorter than cut-off length

[Dallas B. Warren]

> During my MD simulation, the following message was reported: 
> Fatal error: One of the box vectors has become shorter than 
> twice the cut-off length Although I've tried different box 
> dimensions manually, but from ngmx I can always see my 
> protein move out of the box in one direction and cause the 
> crash. My step size is 2 fs, and initial structure of protein 
> has been energy minized.The comm_mode I chose was Linear, 
> shoul I change to Angular?

That has nothing to do with your protein "moving out of the box in one
direction".  That will not cause the crash, since most likely you have a
periodic boundary condition in place.  That means anything that passes
out one side of the box comes back into the box on the opposite face.

Your issue here is that either the x, y or z dimension of the box has
gone underneath the cut-off length for the electrostatics that you have
specified.  It is probably something of the order of 1.5 nm, so one of
those dimensions has gone under 3nm.  Solution, make your box bigger so
that it doesn't reach that limit.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.