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On 12/08/2011 11:09 PM, Kavyashree M wrote:
<blockquote
cite="mid:CAPLGqjrb9FFOLxDEzQK5+WXPE+EFdYy1-E-o3KXT-SwaA+BOsQ@mail.gmail.com"
type="cite">Sir, <br>
<br>
Yes I was the one who posted that. I understand that, I had used <br>
dodecahedron and the problem here is- since i need to compare <br>
these simulations is it ok if i increase the size of the box for
only this<br>
system (which is problematic) and redo the simulation or do i need
to <br>
do for all 16. I hope my i am putting the question clearly.<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPLGqjrb9FFOLxDEzQK5+WXPE+EFdYy1-E-o3KXT-SwaA+BOsQ@mail.gmail.com"
type="cite"><br>
Thank you<br>
with regards<br>
Kavya<br>
<br>
<div class="gmail_quote">On Fri, Aug 12, 2011 at 6:22 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
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0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
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<div class="h5"><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Dear users,<br>
<br>
I have done some 16 simulations of a protein with
mutations,<br>
by keeping the distance between protein atom and the
simulation<br>
box to be 1.0nm (i.e, -d option in editconf) but only in
one of the<br>
simulation I found violation of minimum image distance.
So Should<br>
I increase the box size only for this or should I
increase for all and<br>
redo the simulations?<br>
<br>
</blockquote>
<br>
</div>
</div>
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).<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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