Dear users,<br><br> While analyzing an MD simulation run for 100ns, for temperature,<br>pressure, volume and density, I got an output like this - <br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Temperature 300 9e-05 -nan -0.000501989 (K)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Pressure 0.99914 0.027 -nan 0.0174391 (bar)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Volume 517.755 0.0094 -nan 0.010871 (nm^3)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Density 1012.53 0.018 -nan -0.0216399 (kg/m^3)<br><br>Why is "nan" being shown for RMSD? <br>when I checked the rmsd plot for the backbone, it had equilibrated 6ns,<br>
later on there were fluctuations. <br><br>When I observed the trajectory in ngmx, after some time the protein molecule<br>(the system consistes of 1 intact protein chain in water with few ions to neutralize<br>the charge) appeared fragmented. when I used the command <br>
"trjconv -s protein.tpr -f traj.xtc -o traj_atom.xtc -pbc nojump"<br>the entire molecule was intact throughout the simulation but was going out of the <br>box. <br><br>I had used dodecahedron cell for simulation this option was not present in gnmx-<br>
box display options. Does the type of box selected in ngmx has effect on whether<br>molecule is inside the box or outside? <br><br>What I need to do to keep the molecule in the box and completely inside the box?<br>(I tried with -pbc options atom, res, mol - protein was in fragments in all of them)<br>
<br>How can I visualize a dodecahedron box in ngmx?<br><br>Thanking you<br>With Regards<br>M. Kavyashree<br>