From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Sat Jun 02 2012 - 12:36:14 CDT

Have you checked the periodic boundary conditions?

Anurag

On Sat, Jun 2, 2012 at 10:41 AM, patrick wintrode <pat_wde2_at_yahoo.com>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?
>
> Thanks.
>
> Patrick L. Wintrode
> School of Pharmacy
> University of Maryland
>