[gmx-users] Simulation of Small Water Box

Justin Lemkul jalemkul at vt.edu
Fri May 3 12:08:18 CEST 2013

On 5/3/13 5:41 AM, Monoj Mon Kalita wrote:
> Dear Users
> Can Anybody help me to simulate a water box with nearly 14.45 A  box size
> and approximately 93 water molecules. I have tried to simulate it using the
> 'spc' water model. I have done the SD and CG minimization step. Till that
> step it was fine, but when I tried to do MD then I got the following error
> message
> *One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off.*
> Is there any well established method to simulate a small water box nearly
> of the size I have mentioned? It would be great if I could get it. Have a
> nice day.

The error warns you that you are violating the minimum image convention.  For a 
system of such a tiny size, fluctuations in the box vectors that arise from 
pressure coupling can be quite significant.  Unless you are using a cutoff of 
0.7 nm or less (which would be incorrect to do, as you will have serious cutoff 
errors), you cannot use a box this small.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list