[gmx-users] PBC treatment: need an explanation

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 24 13:17:37 CEST 2012

Hi Anna,

If there is a representation in which the units are together, then
they're together. Trjconv can't put things together which are, in
fact, separated.



On Tue, Apr 24, 2012 at 12:51 PM, Anna Marabotti
<anna.marabotti at isa.cnr.it> 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? 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
> ____________________________________________________
> 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
> man"
> (Roberto Benigni, about Roberto Saviano)
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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