[gmx-users] trjconv options?

Timofey Tyugashev tyugashev at niboch.nsc.ru
Wed Feb 3 12:33:08 CET 2016

Thank you for replies on my previous questions.
And now I have another one dealing with trjconv.

I have a simulation of  a three-chain protein/nucleic acid complex. 
Naturally, it gets broken in three separate strands by PBC.
After trying several, I settled on using options '-pbc mol' with '-ur 
compact' which makes the complex look decent again and it looks like 
that does the job.
But I'm worried about a possibility of something getting unrepaired by 
this option and getting unnoticed by me. What is the way to check for it?
Also it keeps tumbling around the cell during the trajectory. It's 
annoying. Is there a way to pin down the cluster and stop it from rotating?

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