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<DIV><FONT size=2 face=Arial><SPAN class=828441910-24042012>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=828441910-24042012>I know that this is
one of the most frequent subjects in the gmx-users list, however please let me
ask you for a direct answer, since it seems to me that this particular question
was not treated before.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=828441910-24042012></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=828441910-24042012>I'm performing MD
simulations on a dimeric protein, using a rhombic dodecahedric box. I made 3
simulations in which my system was subjected to different isotropic
pressures (first simulation: room pressure; second simulation: small
increase of pressure; third simulation: big increase of pressure). I run 50 ns
simulation for each system, and at the end of simulations I checked for the
visualization of the system with VMD and for the RMSD against the starting
configuration.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=828441910-24042012>Using g_rms command,
I checked for the backbone RMSD against starting structure (fullMD.tpr file).
The first system stabilized after a few ns of simulation, and then the RMSD
remained constant. The second system stabilized after a few ns of simulation,
but with a quantity of "spikes". The third system stabilized after a few ns of
simulation and then, at about 30 ns of simulation, the RMSD value jumped on from
approx. 0.4 nm to > 4 nm and stayed stable on that new value until the end of
simulation.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=828441910-24042012>I had a look at this
trajectory with VMD, and saw that the dimeric protein separates into two
monomers. This phenomenon is consistent with some experimental data about the
protein, and it seems to me consistent also with the RMSD trend found on the
trajectory. However, due to visualization problems with my rhombic system, I
decided to apply trjconv -pbc nojump:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=828441910-24042012></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=828441910-24042012>trjconv -s
fullMD.tpr -f fullMD.xtc -o fullMD_noj.xtc -pbc nojump</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=828441910-24042012>(choosing System=0
as option)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><SPAN class=828441910-24042012><FONT size=2 face=Arial>After this action, I
re-calculated the RMSD of the simulations using the same options as before...and
found that in the third simultion the RMSD is no longer jumping on to > 4 nm.
The visualization of the trajectory shows the protein in form of a dimer that
fluctuates into the zone of "spreaded" solvent (no longer a
box).</FONT></SPAN></DIV>
<DIV><SPAN class=828441910-24042012><FONT size=2
face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN class=828441910-24042012><FONT size=2 face=Arial>My question is: was
the separation into two monomers a simple artifact of the simulation, corrected
by trjconv, or is trjconv able to affect the results of the system in
such a way that when monomers truly separate, trjconv is able to "force" them
together again? How can I check for these two possibilities? Finally: in this
last case, can you suggest me other ways to manage the trajectories in order to
remove the spikes related to jump across the periodic
boundaries?</FONT></SPAN></DIV>
<DIV><SPAN class=828441910-24042012><FONT size=2
face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN class=828441910-24042012><FONT size=2 face=Arial>Thank you very much
for help, and best regards</FONT></SPAN></DIV>
<DIV><SPAN class=828441910-24042012><FONT size=2
face=Arial>Anna</FONT></SPAN></DIV>
<DIV><SPAN class=828441910-24042012></SPAN><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 page: <A
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 a gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV>
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