VMD-L Mailing List

From: patrick wintrode (pat_wde2_at_yahoo.com)
Date: Sat Jun 02 2012 - 11:41:04 CDT

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