[gmx-users] Problems with trajectories

Steve Seibold stevesei at ymail.com
Mon May 26 22:01:31 CEST 2014

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..


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