[gmx-users] correction for minimum image distance violation
Mark.Abraham at anu.edu.au
Fri Aug 12 15:34:23 CEST 2011
On 12/08/2011 11:09 PM, Kavyashree M wrote:
> 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.
> Thank you
> with regards
> 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 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
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