<div dir="ltr">Thank you so much Tobias, Marcella and Prof. Petkov!! I am now able to view my molecule inside the simulation box :)<div><br></div><div>Best regards,</div><div>Megha</div><div><br></div><div><br></div><div><br>On Tuesday, October 25, 2016 at 3:29:08 AM UTC-4, petkov wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"> <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" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcomputationalcatalysis.eu%2FJoomla_1.6.1%2Findex.php%2Fassis-prof-dr-petko-st-petkov\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEJepiO9ori8k1EJhtJDwmIwLXenw';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcomputationalcatalysis.eu%2FJoomla_1.6.1%2Findex.php%2Fassis-prof-dr-petko-st-petkov\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEJepiO9ori8k1EJhtJDwmIwLXenw';return true;"> http://computationalcatalysis.<wbr>eu</a></div> <div align="left">==============================<wbr>=</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 <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="NgjlEiNICQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">marc...@gmail.com</a>><br> To: cp2k <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="NgjlEiNICQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>><br> Date: Tue, 25 Oct 2016 00:00:02 -0700 (PDT)<br> Subject: [CP2K:8295] Re: visualizing geometry from *-<a href="http://pos-1.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fpos-1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDt7CsKeVnFOHZuhRT_3-eMiD3pQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fpos-1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDt7CsKeVnFOHZuhRT_3-eMiD3pQ';return true;">pos-1.xyz</a> 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><a href="http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fplugins%2Fpbctools%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGJrBjAMgOql4m5N5ip_uyQDScgcw';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fplugins%2Fpbctools%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGJrBjAMgOql4m5N5ip_uyQDScgcw';return true;">http://www.ks.uiuc.edu/<wbr>Research/vmd/plugins/pbctools/</a></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 rel="nofollow" href="http://pos-1.xyz" target="_blank" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fpos-1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDt7CsKeVnFOHZuhRT_3-eMiD3pQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fpos-1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDt7CsKeVnFOHZuhRT_3-eMiD3pQ';return true;">pos-1.xyz</a> file generated by CP2K. How do I see these geometry changes in *-<a rel="nofollow" href="http://pos-1.xyz" target="_blank" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fpos-1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDt7CsKeVnFOHZuhRT_3-eMiD3pQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fpos-1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDt7CsKeVnFOHZuhRT_3-eMiD3pQ';return true;">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> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="NgjlEiNICQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;"> cp2k+un...@googlegroups.<wbr>com</a>.<br> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="NgjlEiNICQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;"> c....@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/group/cp2k';return true;" onclick="this.href='https://groups.google.com/group/cp2k';return true;"> https://groups.google.com/<wbr>group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/optout';return true;" onclick="this.href='https://groups.google.com/d/optout';return true;"> https://groups.google.com/d/<wbr>optout</a>.<br> </blockquote> </blockquote></div></div>