[gmx-users] bilayer thickness 100ns membrane protein

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Tue Sep 18 07:25:03 CEST 2018

Dear Stephani,
                       Can u please tell me how you did the simulation and
what forcefield you used for your system. Did you followed the same
tutorial explained by justin lemkul

On Sun, Sep 16, 2018 at 9:46 PM, Stephani Macalino <
stephanimacalino at gmail.com> wrote:

> 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
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