<div>Hi Justin,</div>
<div> </div>
<div>Do you have any clue of this problem? You are the last hope, please help :)</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Fri, Oct 28, 2011 at 2:45 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>With other residues is the same... and changes are bigger. Which trajectory in this case is reliable?</div>
<div> </div>
<div>My wsteps in trjconv involves:</div>
<div> </div>
<div>
<p style="MARGIN: 0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span><font size="3">1.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">First make your molecules whole if you want them whole (system).</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font face="Times New Roman"><font size="3"></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span><font size="3">3.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span><font size="3">4.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Remove jumps if you want to have them removed using the first frame</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span><font size="3">5.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Center your system using some criterion. Doing so shifts the system, so don't use </font></font><code><span style="FONT-SIZE: 10pt">trjconv -</span></code><span><span style="BACKGROUND: yellow"><font size="3" face="Times New Roman">pbc</font></span></span><code><span style="FONT-SIZE: 10pt"> nojump</span></code><font size="3" face="Times New Roman"> after this step.</font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span><font size="3">6.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Put everything in some box.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"> </p>
<p style="MARGIN: 0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span><font size="3">7.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Fit if desired and don't use any <span><span style="BACKGROUND: yellow">PBC</span></span> related option afterwards.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p><br></div>
<div>
<div></div>
<div class="h5">
<div class="gmail_quote">On Fri, Oct 28, 2011 at 2:28 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>Dear Gmx Users,</div>
<div> </div>
<div>I have compared average number of hbonds per time frame between my ligand and protein:</div>
<div> </div>
<div>1) Using trajectory obtained straight after simulations:</div>
<div> </div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US">g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg</span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US"></span> </div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US">Avergage number of hbonds: 0.146</span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US"></span> </div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US">2) Using trajectory modified by trjconv according to the PBC workflow on <a href="http://www.gromcacs.org/" target="_blank">www.gromcacs.org</a> :</span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US"><span lang="EN"></span></span> </div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US"><span lang="EN">g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg</span></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US"><span lang="EN"></span></span> </div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US"><span lang="EN"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt" lang="EN-US">Avergage number of hbonds: 0.156</span></span></span></div>
<p>Does anyone know why this value changed and I obtained slightly different results?</p>
<p>Thank you,</p>
<p>Steven</p></blockquote></div><br></div></div></blockquote></div><br>