<br><br>
<div class="gmail_quote">On Mon, Jan 30, 2012 at 1:46 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:
<div>
<div class="h5"><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br><br>On Mon, Jan 30, 2012 at 12:16 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>> wrote:<br>
<br> On 30/01/2012 8:43 PM, Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"> Dear Gmx Users,<br> I run the simulation of protein with 10 ligands (200 ns). In total<br> I should have total of 4000 frames as I set up:<br>
<br> nsteps = 100000000<br><br> dt = 0.002<br><br> nstxout = 25000<br><br></blockquote><br> ... iff the simulation completed successfully.<br><br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"> I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump<br><br> The trajectory which I read in VMD has 3008 frames and my ligands<br>
completely disappear after 8 frame (They are not in PBC windows<br> which I checked in Graphics -> Graphical Representation -> Periodic)<br><br></blockquote><br> Your choice of trjconv workflow demands that the protein be allowed<br>
to diffuse away. What VMD makes of that is not really of consequence<br> to discuss here. Perhaps you can design a better trjconv workflow,<br> as here<br> <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/<u></u>Documentation/Terminology/<u></u>Periodic_Boundary_Conditions</a><br>
<br><br> Thank you. I managed to fix it using:<br> trjconv -f md.trr -o md1000.xtc -skip 4 (1000 frames instead of 4000)<br> Then accoring to the workflow (PBC) I used:<br> <br>trjconv -f md1000.xtc -s md.tpr -pbc mol -o mdmol.xtc <br>
trjconv -f mdmol.xtc -s md.tpr -center -o mdCENTER.xtc (Center on a protein, output - System)<br> <br>trjconv -f mdCENTER.xtc -s md.tpr -fit rot+trans -o mdFit.xtc (Protein, output - System)<br><br> <br>However, all ligands jump rapidly<br>
<br> 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?<br>
<br> <br></blockquote><br></div></div>Is this unusual? It sounds like the molecules diffuse around until they bind to the protein. You're centering on the protein and then fitting its translation and rotation; everything else will be processed relative to those criteria.<br>
<br>-Justin<br><br></blockquote>
<div>Sorry, I did not clarify it properly. What is unusual is that </div>
<div>my ligands (until they bind) jump to its periodic images. It is a speed light diffusion :) Any suggestions?</div>
<div> </div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">-- <br>==============================<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>==========
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