[gmx-users] Problems with trajectories

Justin Lemkul jalemkul at vt.edu
Mon May 26 23:13:45 CEST 2014

On 5/26/14, 3:39 PM, Steve Seibold wrote:
> I REALLY need some help here. I have tried for several days now and looked on line to fix the situation. My protein moves around and goes outside the simulation waterbox and my Zinc ions also frequently have bonds to protein of 40 angstroms are so.
> Here is one of the combinations I have tried so far to remove translational motion of protein and keep it in the center of the box:
> trajconv  -f pr13.trr ( traj. file containing the last 8 ps) -s pr1.tpr (containing the first pdb structure before any MD, but with waters etc) -pbc atoms (place all atoms into center of box) -center -boxcenter tric -o protein13.trr
> This  results in protein no longer separating into parts (pieces), but protein moves, still all over the box and outside of the box..and Zincs still have long bonds...
> Then, I use 'fit' as follows in an attempt to do a least squares fit of all trajectories (positions) back onto initial structure which is in center of box.....
> trajconv -s pr1.tpr -f protein13.trr (using the output from above) -fit progressive -o protein13A.trr
> This didn't help at all..
> I am really at a loss here on how to deal with this and could use some help..

For a protein in a box of water, a simple trjconv -pbc mol -ur compact -center 
almost always works.  In diagnosing trjconv issues, providing images of outcomes 
from the listed commands is incredibly helpful; "didn't help at all" is not 
exactly diagnostic or very useful.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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