From: Axel Kohlmeyer (
Date: Sat Jun 02 2012 - 12:38:42 CDT

On Sat, Jun 2, 2012 at 12:41 PM, patrick wintrode <> wrote:
> Hi.
> I loaded the .gro and .trr files from a gromacs simulation. In a few
> frames in the middle of the trajectory, several atoms (from multiple parts
> of the structure) stretch out about 20 angstroms from the body of the
> protein and then "snap" back into place.
> When I look at the potential energy from the simulation using g_energy and
> the .emd file, there are no crazy spikes in the energy that would reflect
> such behavior (and in any case I suspect the simulation should have crashed
> if the structure was distorted that badly). So I'm not sure whether what I'm
> seeing is "real" or an artifact that occurs when loading the trajectory into
> vmd.
> Have people seen this before when vmd is used with gromacs files?

this kind of effect only has been reported on this
mailing list a gazillion times. you have bonded atoms
cross periodic boundaries on a trajectory file where
atoms (or rather charge groups in the case of gromacs)
are wrapped back into the principal simulation cell.

it has nothing to do with VMD.

> Thanks.
> Patrick L. Wintrode
> School of Pharmacy
> University of Maryland

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.