Hello I am running a simulation with charge and without charge for 128 pairs of bmim-tf2n ioinc liquids. This is the command for the original run without charge mdrun -s gs.tpr -o gs.trr -c 0.pdb -e gs.edr -g gs.log -pd -nt 8 This is the command for the rerun with charge mdrun -s es.tpr -o es.trr -c 0.pdb -e es.edr -g es.log -rerun gs.trr -pd -nt 8
In the original trajectory, the energy of the system fluctuates around 5000 kJ/mol. In the rerun trajectory, the energy of the system also mostly fluctuates around 5000 kJ/mol, but sometimes it jumps to 10^13 or 10^-13. In the most recent run (20 ns), 16 data points out of 2000000 were extremely large. Checking the trajectory files, it seems like caused by molecule stretching across the pbc. Nilesh -- 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
