[gmx-users] bilayer thickness 100ns membrane protein

[Stephani Macalino]

Hello,
I ran a 100ns MD or a membrane protein and am now analyzing the APL and
bilayer thickness from the trajectory file of 50,000 frames.
When I graphed the values, around 20 to 30k frames in (and some frames
along 40k) the value jumps from 40 to 70. The rest of the frames have
pretty similar value at 40.
Can you provide any idea why this happens?
I already used trjconv in for my system before doing this.
Should I run it for a longer time?
Hope you can help. Thank you!
Regards,
Stephani