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On 30/01/2012 8:43 PM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQHwYSk=bdsWvs_Lc_a=r_LmZBCRnE6YHQwdMU1A_+ZkKg@mail.gmail.com"
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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>
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<br>
... iff the simulation completed successfully.<br>
<br>
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<div><span lang="EN">
<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>
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<br>
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">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>
<br>
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<div><span lang="EN">
<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>
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<br>
trjconv -h<br>
<br>
Mark<br>
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<div><span lang="EN">
<p>Thank you,</p>
<p> </p>
<p>Steven</p>
</span></div>
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