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<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN class=953460015-20122011>When I obtained
trajectories, I used trjconv to reset the visualization of my
systems:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN class=953460015-20122011>editconf -f traj.tpr
-o traj_0ns.gro</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN
class=953460015-20122011>then:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>In order to manage
this issue, I applied nojump to the trajectory of this "anomalous"
system:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>trjconv -f
traj_mol.xtc -s traj.tpr -pbc nojump -o traj_molnoj.xtc</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>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 size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>What I would like to
know is:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>- Did I make the
correct procedure to treat these systems?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>- Can I compare the
results obtained on this -mol + -noj trajectory with the other trajectories -mol
only?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>- 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 size=2 face=Arial><SPAN
class=953460015-20122011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>Any help would be
very appreciated.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=953460015-20122011>Many thanks in
advance and best regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=953460015-20122011>Anna</SPAN></FONT></DIV>
<DIV align=left>
<DIV dir=ltr align=left><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web site: <A
title=http://bioinformatica.isa.cnr.it/anna/anna.htm
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 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 size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV></DIV>
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