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><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 href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><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>
==============================<u></u>==========<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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></blockquote></div><br>