[gmx-users] MD - analysis

[Kavyashree M]

Dear users,

    While analyzing an MD simulation run for 100ns, for temperature,
pressure, volume and density, I got an output like this -

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Temperature                     300      9e-05       -nan -0.000501989  (K)

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                    0.99914      0.027       -nan  0.0174391  (bar)

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Volume                      517.755     0.0094       -nan   0.010871  (nm^3)

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Density                     1012.53      0.018       -nan -0.0216399
(kg/m^3)

Why is "nan" being shown for RMSD?
when I checked the rmsd plot for the backbone, it had equilibrated 6ns,
later on there were fluctuations.

When I observed the trajectory in ngmx, after some time the protein molecule
(the system consistes of 1 intact protein chain in water with few ions to
neutralize
the charge) appeared fragmented. when I used the command
"trjconv -s protein.tpr -f traj.xtc -o traj_atom.xtc  -pbc nojump"
the entire molecule was intact throughout the simulation but was going out
of the
box.

I had used dodecahedron cell for simulation this option was not present in
gnmx-
box display options. Does the type of box selected in ngmx has effect on
whether
molecule is inside the box or outside?

What I need to do to keep the molecule in the box and completely inside the
box?
(I tried with -pbc options atom, res, mol - protein was in fragments in all
of them)

How can I visualize a dodecahedron box in ngmx?

Thanking you
With Regards
M. Kavyashree
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