[gmx-users] trjconv problems

Steve Seibold stevesei at ymail.com
Wed May 28 18:19:11 CEST 2014

I have been working on post modifying my trajectories using trjconv. My protein has two zinc ions, and I have used PBC (explicit waters). After a week of attempting to get my simulations to behave due to boundary effects, I have finally got my protein to not fall apart, and even managed to get the waters to stay within the box (visually using VMD). However, the problem now is my zinc ion ligands.
To simplify my problem with the zincs, I removed the waters (using  groups in my index file). I then created a group in the index called "protein_ZN" which contain protein and two zinc atoms..this did work..Then I did the following:

trjconv -s pr.trp -f pr13.trr -pbc nojump -n index.ndx -o protein13.trr: The output group was "protein_zn".


trjconv -s pr.trp -f protein13.trr -n index.ndx -fit rot+trans -o protein13A.trr

When I visualized the  traj. in VMD it showed that this worked, but only for ONE zinc ligand ion...the other left the box with ligand to sulfur bond on 30-40 angstroms.

Can someone tell me what is going on here...???

Thanks, Steve 

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