[gmx-users] bilayer thickness 100ns membrane protein

[Stephani Macalino]

Hello,
Thanks for the response. But I have already done the trjconv pbc whole,
nojump and center for my system to possibly fix this. Lemme try to check
again from my orig trajectory file.
Then I will get back to you.
Thank you!

On Mon, Sep 17, 2018, 01:27 Justin Lemkul <jalemkul at vt.edu> wrote:

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