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<div class="gmail_quote">On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br><br>Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">Dear Gmx Users,<br> I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow:<br> <br>1. First make your molecules whole if you want them whole<br>
<br>trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc<br><br>2. Cluster your molecules/particles if you want them clustered<br><br>3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps.<br>
<br>trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb<br><br>4. Remove jumps if you want to have them removed using the first frame<br><br>trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc<br>
<br></div>5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step.
<div class="im"><br><br>trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc<br><br>6. Put everything in some box.<br><br>trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc<br><br>
7. Fit if desired and don't use any PBC related option afterwards.<br><br>trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc<br><br> <br>I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions?<br>
<br> <br></div></blockquote><br>Center on either the protein, the ligand, or some custom index group of residues surrounding the ligand. Centering on the whole system usually doesn't do anything useful.<br><br>-Justin<br>
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<div>Thank you guys but...</div>
<div> </div>
<div>I am trying and it does not work... my ligand is jumping like an idiot outside the box changing its position even two dimensions of box in one frame. I removed -ur compact from the first line and I tried centering on ligand or protein (centering group: LIG or Protein, output: SYSTEM). No results... </div>
<div>My ligand at the begining of the simualtion is not within the protein. Please, help :(((( I tried this workflow with many ligands and same protein - it worked! Now it does not...</div>
<div>Here is my workflow:</div>
<div> </div>
<div>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><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.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><font size="3">2.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Cluster your molecules/particles if you want them clustered</font></font></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><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; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><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 (system)</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><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 class="highlight"><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 (tried centering on LIG or PROTEIN)</font></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><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; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><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 class="highlight"><span style="BACKGROUND: yellow">PBC</span></span> related option afterwards.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc</font></font></span></p>
<span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">With point three, the issue is that <a title="Documentation/Gromacs Utilities/trjconv" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv">trjconv</a> removes the jumps from the first frame using the reference structure provided with </span><code><span style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">-s</span></code><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">. If the reference structure (run input file) is not clustered/whole, </span><code><span style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">trjconv -</span></code><span class="highlight"><span style="FONT-FAMILY: 'Times New Roman'; BACKGROUND: yellow; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">pbc</span></span><code><span style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"> nojump</span></code><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"> will undo steps 1 and</span></div>
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<div>Steven</div>
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<div>==============================<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> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><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>========== </div>
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