[gmx-users] bilayer thickness 100ns membrane protein

Justin Lemkul jalemkul at vt.edu
Sun Sep 16 18:26:36 CEST 2018

On 9/16/18 12:16 PM, Stephani Macalino 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.

Have you visualized the trajectory to make sure all molecules were 
imaged appropriately? It sounds to me like your lipids are simply 
jumping across PBC. Sudden jumps or discontinuities in time series are 
almost always due to PBC effects.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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