Kavyashree M wrote:
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?
It means "not a number." I've never seen that before from g_energy, but based
on the extremely small error estimates, especially for the temperature, I'd
suspect you're using extremely tight coupling which may be causing some error.
when I checked the rmsd plot for the backbone, it had equilibrated 6ns,
later on there were fluctuations.
The RMSD presented by g_energy is the standard deviation of the data analyzed.
It is unrelated to the RMSD of the protein.
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?
In a periodic system, there is no such thing as "inside" and "outside" since the
system is infinite.
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)
trjconv -pbc mol -ur compact (and -center if you like).
How can I visualize a dodecahedron box in ngmx?
Never used ngmx, but with the trjconv command I've stated everything should show
up quite nicely in VMD :)
-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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