[gmx-users] bilayer thickness 100ns membrane protein

[Dallas Warren]

Just to reinforce Justin's point, watch the trajectory.  Especially
around the time point at which you have seen the change in the values
obtained.  You can get a lot of information from just watching things,
rather than looking at a number/graph that one of the analysis scripts
spits out.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Mon, 17 Sep 2018 at 08:11, Stephani Macalino
<stephanimacalino at gmail.com> wrote:
>
> 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
> >
> > --
> > ==================================================
> >
> > 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
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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