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<div><font style="font-family:Arial;font-size:10pt;">
<div>Dear Megha, if you want to apply the cell parameters for all
frames in your trajectory, just go to the VMD Main menu -> Extensions
-> Analysis-> Radial Pair distribution function, in the new opened
window "<font style="font-family:Arial;font-size:10pt;"> Radial Pair
distribution function" on the upper left corner click on the Utilities
menu and choose cell parameters, here enter your cell parameters.</font></div>
<div> </div>
<div>Cheers,</div>
<div>Petko</div>
<div> </div>
</font></div>
<div><font size="2">=============================</font></div>
<div align="left"><font size="2">Assist. Prof. Dr. Petko St. Petkov <br />
Faculty of Chemistry and Pharmacy <br />
University of Sofia <br />
1126 Sofia, Bulgaria <br />
tel: +359 2 8161 433 </font><br />
website: <a
href="http://computationalcatalysis.eu/Joomla_1.6.1/index.php/assis-prof-dr-petko-st-petkov">
http://computationalcatalysis.eu</a></div>
<div align="left">===============================</div>
<div> </div>
<blockquote style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px;
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px"> -----Original
Message-----<br />
From: Marcella Iannuzzi <marc...@gmail.com><br />
To: cp2k <...@googlegroups.com><br />
Date: Tue, 25 Oct 2016 00:00:02 -0700 (PDT)<br />
Subject: [CP2K:8295] Re: visualizing geometry from *-pos-1.xyz inside the
box in VMD<br />
<br />
<div dir="ltr">Dear Megha,
<div> </div>
<div>what Tobias replied is correct. More information can be found, for
example, at</div>
<div>http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/</div>
<div>regards</div>
<div>Marcella<br />
<br />
On Tuesday, October 25, 2016 at 8:35:20 AM UTC+2, Tobias Kraemer
wrote:<blockquote style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc
solid;padding-left: 1ex;" class="gmail_quote">
<div dir="ltr">Dear Megha,
<div> </div>
<div> </div>
<div>the pos file doesn't contain any information about the simulation box.
However, you can tell VMD manually what the parameters are. Open the
terminal (Externsions/Tk Console) and type pbc set {a b c alpha beta gamma}
<enter> pbc box_draw.</div>
<div>This should yield the desired result, i.e. the simulation box / unit
cell of lengths a b c and angles alpha beta gamma. I suspect in your case
the cell will be a simple cube of side length a Angstrom. I am not entirely
sure, but I suspect that the box will only be drawn for one frame of the
trajectory, but I don't know if there is a way to fix the box for all
frames. At least for a first visual inspection this should be
sufficient.</div>
<div> </div>
<div>Hope this helps</div>
<div> </div>
<div>Tobias </div>
<div> </div>
<div> </div>
<div><br />
On Tuesday, October 25, 2016 at 1:57:29 AM UTC+1, Megha Anand
wrote:<blockquote style="margin:0;margin-left:0.8ex;border-left:1px #ccc
solid;padding-left:1ex" class="gmail_quote">
<div dir="ltr">Dear CP2K users,
<div> </div>
<div>Forgive me for asking several trivial questions. I am still new to
CP2K. Many thanks to several members of this group because of whom I am able
to take baby steps towards learning this powerful program.</div>
<div> </div>
<div>I am using VMD to visualize the *-<a target="_blank" rel="nofollow"
href="http://pos-1.xyz">pos-1.xyz</a> file generated by CP2K. How do I see
these geometry changes in *-<a target="_blank" rel="nofollow"
href="http://pos-1.xyz">pos-1.xyz</a> file inside the simulation box. Is
there a keyword that allows to print these coordinates inside the simulation
box for each geometry optimization step. I am doing a non-periodic
computation on a diatomic system using MT poisson solver and would like to
get a feel for the spacing between the system and then cell walls.</div>
<div> </div>
<div>Thank you so much for your time and help!</div>
<div> </div>
<div>Best regards,</div>
<div>Megha</div>
</div>
</blockquote></div>
</div>
</blockquote></div>
</div>
<div> </div>
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