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<div class="gmail_quote">On Mon, Jan 30, 2012 at 12:16 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div class="im">On 30/01/2012 8:43 PM, Steven Neumann wrote:
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<div>Dear Gmx Users,</div>
<div> </div>
<div>I run the simulation of protein with 10 ligands (200 ns). In total I should have total of 4000 frames as I set up:<span lang="EN"><span lang="EN">
<p>nsteps = 100000000</p>
<p>dt = 0.002 </p></span>
<p>nstxout = 25000</p></span></div></blockquote><br></div>... iff the simulation completed successfully.
<div class="im"><br><br>
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<p>I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump</p>
<p>The trajectory which I read in VMD has 3008 frames and my ligands completely disappear after 8 frame (They are not in PBC windows which I checked in Graphics -> Graphical Representation -> Periodic)</p></span></div>
</blockquote><br></div>Your choice of trjconv workflow demands that the protein be allowed to diffuse away. What VMD makes of that is not really of consequence to discuss here. Perhaps you can design a better trjconv workflow, as here <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a>
<div class="im"><br></div></div></blockquote>
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<div> Thank you. I managed to fix it using:</div>
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<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL">trjconv -f md.trr -o md1000.xtc -skip 4<span style> (1000 frames instead of 4000)</span></span></div>
<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL"><span style></span></span> </div>
<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL"><span style><font color="#000000">Then accoring to the workflow (PBC) I used:</font></span></span></div>
<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL"><span style><font color="#000000"></font></span></span> </div>
<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL"><span style><font color="#000000">
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red">trjconv -f md1000.xtc -s md.tpr -pbc mol -o mdmol.xtc<span style> </span></span></p></font></span></span></div>
<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL"><span style></span></span> </div>
<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL"><span style><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt">trjconv -f mdmol.xtc -s md.tpr -center -o mdCENTER.xtc (Center on a protein, output - System)</span></span></span></div>
<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL"><span style><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt"></span></span></span> </div>
<div><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt" lang="PL"><span style><span style="FONT-FAMILY:'Times New Roman';COLOR:red;FONT-SIZE:12pt">
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red">trjconv -f mdCENTER.xtc -s md.tpr -fit rot+trans -o mdFit.xtc (Protein, output - System)</span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font color="#000000">However, all ligands jump rapidly</font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font color="#000000"> around the protein till the time they bind to the protein surface (and the begining they were randomly placed around the protein) one by one. At the end when all of them stacked on my protein everything is ok. Will you suggest something?</font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font color="#000000"></font></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font color="#000000">thank you,</font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font color="#000000"></font></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font color="#000000">Steven</font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red"><font color="#000000"></font></span> </p></span></span></span></div>
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<div class="im"><br>
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<p>Can you please advise? I think I have to many frames in my trajectory, how can I reduce it in trjconv?</p></span></div></blockquote><br></div>trjconv -h<br><br>Mark<br>
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<p>Thank you,</p>
<p> </p>
<p>Steven</p></span></div><br>
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