[gmx-users] membrane pre-equilibration
Kevin Boyd
kevin.boyd at uconn.edu
Mon Oct 8 19:39:04 CEST 2018
Hi,
I'm not exactly sure what you're asking. In both cases (with protein or
without protein), the charmm-gui provides you files which need to be
minimized and equilibrated. Typically, the steps recommended in the README
file are sufficient. The only requirement of these steps it to make your
simulation numerically stable for production runs - so the question of "is
it equilibrated" enough should be more of "does my simulation crash when I
take off the restraints".
Once you have a production run going (i.e. proper temperature and pressure
coupling, no equilibration-style restraints), some portion of that should
be tossed as further equilibration. How much to set aside depends on what
you are trying to measure, and whether equilibration artifacts will affect
that property. For anything that you're trying to measure, you should see
how your observed quantity varies with time.
Kevin
On Mon, Oct 8, 2018 at 2:48 AM Olga Press <pressol at post.bgu.ac.il> wrote:
> 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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