Re: [gmx-users] MD - analysis
Kavyashree M wrote: Dear Sir, g_mindist analysis showed the violation of minimum image convention, it was violated over a short period of time and then it came back to normal. I attach the plot herewith. Should this data be discarded or any useful information can be obtained. You've got a considerable number of data points wherein the periodic image distance is less than the longest cutoff, so I don't think you can simply shrug this off. The data were influenced by spurious interactions. Watch the trajectory, see what's happening during this period, and accommodate for such events in a new simulation based on what you learn. -Justin Thank you With Regards M. Kavyashree -- 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 -- gmx-users mailing listgmx-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
[gmx-users] MD - analysis
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 --- Pressure0.99914 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 listgmx-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
Re: [gmx-users] MD - analysis
Dear Sir, g_mindist analysis showed the violation of minimum image convention, it was violated over a short period of time and then it came back to normal. I attach the plot herewith. Should this data be discarded or any useful information can be obtained. Thank you With Regards M. Kavyashree attachment: less_than_1.4nm.gifattachment: mindist.gif-- gmx-users mailing listgmx-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
