Justin,<br><br>I've used trjconv -pbc mol -ur compact <br>but the final picture was still wrong :(<br><br>So I think that something happened with my box because<br><br>1- If the cubic representation is set on default why other .gro structures were visualized in VMD in dodecahedral box on default ?<br>
<br>2- Why the pereodic boundaries were distorded in the next stage after NPT (production MD) that my structure were outside the box on half ? I want to point that on MD stage the box were dodecahedral again like in the NVT and other stages but my structure was in wrong position. <br>
<br><br>James<br><br><div class="gmail_quote">2011/10/24 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><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>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Justin, hello!<br>
<br>
<br>
I have forced with some problem during final stage of your turorial.<br>
<br>
I dont know why but after NPT phase my sytem has occured in the standart cubic box instead of dodecahedron (after all previosly phases my system was in correct box).<br>
<br>
So when I've passed my system in the MD stage- it's moved back into normal dodecahedron box but on the placement where previously system was. So as the consequence I've obtained protein in the wrong place ( some of its parts were outside new box )<br>
<br>
I've tried examined why this might occur but have not found possible explanations.<br>
<br>
I've examined box coordinates of the all .gro structurs obtained after each of the stages and all of them contained such box vectors<br>
7.85059 7.85059 5.55120 0.00000 0.00000 0.00000 0.00000 3.92529 3.92529<br>
<br>
As I understood It's correspond to the system in the dodecahedron box but my ntp.gro structure with the same is in the cubic box ( with the above box coordinates as well). Why its might occured and were else information of the box coordinates is present exept of initial structure gro file ?<br>
<br>
</blockquote>
<br></div></div>
You still have a dodecahedral box. The default representation is a simple triclinic cell. A true compact representation can be obtained with:<br>
<br>
trjconv -pbc mol -ur compact<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>
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