[gmx-users] membrane pre-equilibration

[Olga Press]

Kevin thank you for your replay.
I've used charmm-gui membrane builder for membrane only system and not
membrane/protein system.
If I'll use the membrane builder membrane/protein system the
charmm-gui provides me un-equilibrated files which I should equilibrate, so
the question is how do I know that the system is equilibrated? which
analysis should I perform for the membrane and for the protein?
Thank you.
Olga


‫בתאריך יום א׳, 7 באוק׳ 2018 ב-16:44 מאת ‪Kevin Boyd‬‏ <‪
kevin.boyd at uconn.edu‬‏>:‬

> Hi,
>
> You should just use charmm-gui's built in functionality to insert the
> protein, unless you have a good reason not to.
>
> Kevin.
>
> On Sun, Oct 7, 2018 at 7:23 AM Olga Press <pressol at post.bgu.ac.il> wrote:
>
> >  Dear all,
> > I'm new in the field of simulating membrane-protein system in gromacs by
> > using charmm36-ff.
> > I've used charmm-gui membrane builder to contract  pure DOPC bilayer and
> > followed the "README" file.  Which analysis should I perform* before*
> > embedding the protein into the membrane to ensure the
> > membrane pre-equilibration? I would be happy if someone can refer me to
> > protocol or links.
> >
> > Thank you.
> > Olga
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