[gmx-users] bilayer thickness 100ns membrane protein

[Bratin Kumar Das]

Dear Stephani,
                        I tried charmm-gui to pack the lipid bilayer
arround my protein. But charmm gui is giving fatal error. what possible
reason can be there for this fatal error.

On Tue, Sep 18, 2018 at 11:01 AM, Stephani Macalino <
stephanimacalino at gmail.com> wrote:

> 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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