[gmx-users] fluctuation of energy in rerun

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 4 09:11:37 CEST 2013

Seems like a bug. Please open an issue at redmine.gromacs.org, and be sure
to mention the GROMACS version.

Why are you using -pd?
On Sep 4, 2013 2:20 AM, "Nilesh Dhumal" <ndhumal at andrew.cmu.edu> wrote:

> 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list