[gmx-users] correction for minimum image distance violation

Kavyashree M hmkvsri at gmail.com
Fri Aug 12 15:09:27 CEST 2011


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.

Thank you
with regards

On Fri, Aug 12, 2011 at 6:22 PM, Justin A. Lemkul <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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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