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On 31/01/2012 1:07 AM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQEDL+tk=FKEQPTSZS+fma2SkSBcdL_h4EjNrqi1M4Lrpg@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Mon, Jan 30, 2012 at 1:46 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
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
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.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 moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions"
target="_blank">http://www.gromacs.org/Documentation/Terminology/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>
</blockquote>
<br>
If ligand A and B start near each other, and each moves and binds to
the protein but travelling in the opposite direction from the other
ligand, what would you like to see? This kind of simulation is not
like iron filings and a magnet :-)<br>
<br>
Mark<br>
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