[gmx-users] correction for minimum image distance violation

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 12 14:52:01 CEST 2011

Kavyashree M wrote:
> Dear users,
> I have done some 16 simulations of a protein with mutations,
> by keeping the distance between protein atom and the simulation
> box to be 1.0nm (i.e, -d option in editconf) but only in one of the
> simulation I found violation of minimum image distance. So Should
> I increase the box size only for this or should I increase for all and
> redo the simulations?

There was an extensive discussion on this topic a few months back, and I thought 
you had posed the original question.  Transient minimum image violations (only a 
few frames) may not be problematic, but if they are frequent then they can 
negatively influence the system and you'd have to do it over with a bigger box 
(or one with more appropriate symmetry, like a dodecahedron, if you did not do 
so in the first place).



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


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