[gmx-users] bilayer thickness 100ns membrane protein

[Stephani Macalino]

Hello Bratin,
I used charmm-gui to generate the MD input files and used CHARMM36 as
forcefield.
Then I used gromacs for the MD production run for 100ns.
Once I got the trajectory files, I did the membrane analysis using a tcl
script and gridmat.
I followed the gromacs tutorial starting from the minimization.
Regards,
Stephani


On Tue, 18 Sep 2018 at 14:25, Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
wrote:

> 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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