[gmx-users] Pull simulation odditites when viewed in VMD

[Natalie Stephenson]

Hey,

I've been performing a pull simulation of a protein, all seems to work fine however after I convert the .xtc file into seperate .gro files and load those into VMD to visualise the simulation something weird happens.  Every 50 frames or so a random bond within the backbone of the protein (not necessarily near the point of pulling or unfolding) seems to extend and spike out massively from the structure - does anyone know why that would be happening?

Thanks for your help
Natalie


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