[gmx-users] a doubt about pbc nojump or mol or whole

[Tsjerk Wassenaar]

Hi Anna,

Jumps like that are a consequence of PBC. Nothing wrong. Removing jumps
like you did is the proper treatment.

Cheers,

Tsjerk

On Dec 20, 2011 9:27 PM, "Anna Marabotti" <anna.marabotti at isa.cnr.it> wrote:

**
Dear gmx-users,
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.
When I obtained trajectories, I used trjconv to reset the visualization of
my systems:

trjconv -f traj.xtc -s traj.tpr -pbc mol -ur compact -o traj_mol.xtc
(selecting 0=System when prompted)

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).

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):
editconf -f traj.tpr -o traj_0ns.gro
trjconv -f traj_0ns.gro -s traj.tpr -pbc mol -ur compact -o traj_mol.gro
(selecting 0=System when prompted)
then:
g_rms -f traj_mol.xtc -s traj_mol.gro -o traj_mol_rms.xvg (selecting
4=Backbone when prompted)

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.

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.

In order to manage this issue, I applied nojump to the trajectory of this
"anomalous" system:
trjconv -f traj_mol.xtc -s traj.tpr -pbc nojump -o traj_molnoj.xtc

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.

What I would like to know is:
- Did I make the correct procedure to treat these systems?
- Can I compare the results obtained on this -mol + -noj trajectory with
the other trajectories -mol only?
- 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?

Any help would be very appreciated.
Many thanks in advance and best regards
Anna
 __________________________________________________________________
Anna Marabotti, Ph.D.
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm

"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)


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