[gmx-users] correction for minimum image distance violation

[Mark Abraham]

On 12/08/2011 11:09 PM, Kavyashree M wrote:
> Sir,
>
> Yes I was the one who posted that. I understand that, I had used
> dodecahedron and the problem here is- since i need to compare
> these simulations is it ok if i increase the size of the box for only this
> system (which is problematic) and redo the simulation or do i need to
> do for all 16. I hope my i am putting the question clearly.

Since the purpose is to run simulations that satisfy the minimum image 
convention, I would re-run only the one that violated. I would apply 
that lesson in subsequent choices of box size.

Mark

>
> Thank you
> with regards
> Kavya
>
> On Fri, Aug 12, 2011 at 6:22 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     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
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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