<p>Hi Anna,</p>
<p>Jumps like that are a consequence of PBC. Nothing wrong. Removing jumps like you did is the proper treatment.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Dec 20, 2011 9:27 PM, "Anna Marabotti" <<a href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</a>> wrote:<br><br><u></u>
<div>
<div><font face="Arial"><span>Dear
gmx-users,</span></font></div>
<div><font face="Arial"><span>I've just finished
several simulations of 4 single point mutants of my dimeric protein in
rhombic dodecahedron box (-d 1.5 nm) centered on the protein, filled with water,
neutralized with sodium, simulated with Gromacs 4.5.3 for 30 ns after NVT and
NPT dynamics. I made simulations in the same way and with the same settings,
obtaining 4 trajectories.</span></font></div>
<div><font face="Arial"><span>When I obtained
trajectories, I used trjconv to reset the visualization of my
systems:</span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>trjconv -f traj.xtc
-s traj.tpr -pbc mol -ur compact -o traj_mol.xtc (selecting 0=System when
prompted)</span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>then I used
g_mindist to calculate minimum distance between periodic images. The resulting
graphs showed me that for all simulations the distance is never lower than 2.0
nm, but for only one system there are some spikes in the final part of the
simulation (between 25 and 30 ns) lowering the min distance below 1 nm
(only in correspondence of these spikes). </span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>I also calculated
the rmsd using as reference the .gro file obtained in this way (as suggested
sometimes ago by somebody of you, perhaps Justin or Tsjerk):</span></font></div>
<div><font face="Arial"><span>editconf -f traj.tpr
-o traj_0ns.gro</span></font></div>
<div><font face="Arial"><span>trjconv -f
traj_0ns.gro -s traj.tpr -pbc mol -ur compact -o traj_mol.gro (selecting
0=System when prompted)</span></font></div>
<div><font face="Arial"><span>then:</span></font></div>
<div><font face="Arial"><span>g_rms -f
traj_mol.xtc -s traj_mol.gro -o traj_mol_rms.xvg (selecting 4=Backbone when
prompted)</span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>I see a quite stable
rmsd around 0.2 nm for all systems, with spikes up to 4 nm in the same system
that showed problems with g_mindist, in positions corresponding to the
spikes in the g_mindist.xvg graph.</span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>Looking at this
trajectory with VMD, I saw that in correspondence with the spikes, the two
monomers of the protein "dissociate" and appear in different parts of the
simulation box (i.e. my periodic image is formed by one monomer, and another
monomer is seen in correspondence with another periodic image). All the other
systems move into the periodic box, without "dissociating" into
monomers.</span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>In order to manage
this issue, I applied nojump to the trajectory of this "anomalous"
system:</span></font></div>
<div><font face="Arial"><span>trjconv -f
traj_mol.xtc -s traj.tpr -pbc nojump -o traj_molnoj.xtc</span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>When I repeated the
analyses with g_mindist and g_rms, I see graphs perfectly superimposed to the
former graphs, except for spikes that have been disappeared.</span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>What I would like to
know is:</span></font></div>
<div><font face="Arial"><span>- Did I make the
correct procedure to treat these systems?</span></font></div>
<div><font face="Arial"><span>- Can I compare the
results obtained on this -mol + -noj trajectory with the other trajectories -mol
only?</span></font></div>
<div><font face="Arial"><span>- In your
opinion, is the "dissociation" of the two monomers only a problem of
visualization (given that this protein "behaves" apparently normally after
applying pbc nojump), or I have to suppose that this system is anomalous only
for this fact?</span></font></div>
<div><font face="Arial"><span></span></font> </div>
<div><font face="Arial"><span>Any help would be
very appreciated.</span></font></div>
<div><font face="Arial"><span>Many thanks in
advance and best regards</span></font></div>
<div><font face="Arial"><span>Anna</span></font></div>
<div align="left">
<div dir="ltr" align="left"><font face="Arial">__________________________________________________________________</font></div>
<div align="left"><font face="Arial">Anna Marabotti, Ph.D.</font></div>
<div align="left"><font face="Arial">Web site: <a title="http://bioinformatica.isa.cnr.it/anna/anna.htm" href="http://bioinformatica.isa.cnr.it/anna/anna.htm" target="_blank">http://bioinformatica.isa.cnr.it/anna/anna.htm</a></font></div>
<div align="left"><font face="Arial"></font> </div>
<div align="left"><font face="Arial">"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</font></div>
<div align="left"><font face="Arial">(Roberto Benigni, about Roberto
Saviano)</font></div></div>
<div> </div></div>
<br>--<br>
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