[gmx-users] Box vector error

Prem Singh Kaushal ps at mbu.iisc.ernet.in
Wed Oct 21 10:18:03 CEST 2009

Dear All

     I am using GROMCS 3.3.1 version. I had started the simulation of protein in
water with an octahedral box of dimension 9.76276   9.20449   7.97128   0.00000 
 0.00000   3.25425   0.00000  -3.25425  4.60225. However after 25ns the
simulation aborts with the following error:

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or one
of the box diagonal elements has become smaller than the cut-off.
The box size at this pint is

At this time point box has changed drastically with vectors,   2.61137  15.10480
 18.99570   0.00000   0.00000   0.00002   0.00000   0.00002   0.00003.

I tried to restart simulation, going back,  from the time point where there was
no substantial change in the dimensions of the box, but simulations aborts again
after some time with the same error. The time points at which simulation aborts
are random. Having simulated for 25ns now i do not want to change the box shape
and resimulate everything again.

I shall appreciate you prompt suggestions regarding this.

With regards

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