[gmx-users] correction for minimum image distance violation

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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