On 4/24/12 6:51 AM, Anna Marabotti wrote:
Dear gmx-users,
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.
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.
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.
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:
trjconv -s fullMD.tpr -f fullMD.xtc -o fullMD_noj.xtc -pbc nojump
(choosing System=0 as option)
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).
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?
The real answer is "neither." The results you obtained are not an artifact;
they are normal behavior for a periodic cell. The visual representation created
by trjconv was simply a re-wrapping of periodic boundaries so that it was more
convenient.
If the monomers truly separated, there is no way trjconv (through the simple use
of -pbc options) can force them back together. There are many ways in which the
user can manipulate coordinates; this isn't one of them.
You can check the stability of the dimer interactions in a number of ways -
hydrogen bonds (g_hbond), distances (g_dist), contacts (g_mindist), etc.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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