[gmx-users] PBC treatment: need an explanation

Anna Marabotti anna.marabotti at isa.cnr.it
Tue Apr 24 12:51:22 CEST 2012

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? 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?
Thank you very much for help, and best regards
Anna Marabotti, Ph.D.
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with a gun is a dead
(Roberto Benigni, about Roberto Saviano)
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