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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
