[gmx-users] membrane-protein system by using charmm36 ff

[Shreyas Kaptan]

Hi.

it is quite important that you do a pre-equilibration generally. This is
assuming that you are starting with membranes built from scratch. If you
have a patch that you obtained from charmm-gui website or other sources
that someone has previously equilibrated, then, of course, you can forgo
the pre-equilibration. The reason pre-equilibration is so important is that
membranes generated by insertion methods tend to have a lot of clashes. NVT
simulations (even short ones, approx. 1ns) ensure that given a box size you
can accommodate the lipids and relax them before you attach the pressure
coupling.

An equlibration of 200-300 ns *might* be an overkill if your protein does
not have a too large hydrophobic mismatch. but of course, more
equilibration only helps. Once again, use parameters appropriate for the
system to determine if the equilibration is enough instead of using some
default timescale.

Shreyas

On Mon, Jun 18, 2018 at 10:51 AM Olga Press <pressol at post.bgu.ac.il> wrote:

> Thank you for your help!
> How important is it to make a good pre-equilibration before embedding a
> protein into the membrane if I'm going to perform long (200-300ns)
> equilibration of the whole system (mempare+protein) using NVT followed by
> NPT ensemble before production of MD simulation?
> Thank you all for your help.
>
>
> Olga
>
>
>
>
> 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan <shreyaskaptan at gmail.com>:
>
> > Hi.
> >
> > Maybe you already know this but you can also build the whole embedded
> > system with charmm-gui. Also, your parameters appear reasonable to me at
> > first glance.
> >
> > As for the equilibration, that is a system specific question. If you
> have a
> > "simple" uniform lipid content in the bilayer I would say from my
> > experience, that the equilibration depends on the lipid heads and tails.
> > Large heads and long tails generally imply a longer equilibration. Mixed
> > lipids can require up to "microseconds" worth of equilibratio. I would
> take
> > the saturation to a nearly fixed value of the Area per lipid and the
> > bilayer thickness as an indication that it is safe to consider the
> > "equilibration" enough.
> >
> > Do not use the 0.495 ns as some timescale. It is in fact quite short.
> >
> >
> >
> > On Sun, Jun 17, 2018 at 1:25 PM Olga Press <pressol at post.bgu.ac.il>
> wrote:
> >
> > > Dear Gromacs users,
> > > I'm new in the field of Molecular Dynamics especially in using Gromacs.
> > > I have several questions regarding mdp file and I'll be very grateful
> if
> > > you can help me with them.
> > > I'm using a membrane-protein system with Charmm36 ff. After I have
> > > constructed bilayer membrane by using CHARMM-GUI membrane builder I
> have
> > > run the README file as it, without changing the equilibration time
> (total
> > > equilibration time of 0.475ns). Followed by embedded protein into the
> > > membrane by using g_membed and performed solvation and minimization of
> > the
> > > entire system as was described in the KALP15-DPPC  tutorial by Dr.
> Justin
> > > A.Lemkul.
> > >
> > > those are my questions:
> > > 1. Does the pre-equilibration of 0.475ns is enough before embedding
> > protein
> > > into the membrane and followed by long equilibration of the whole
> system
> > > for 200ns  by using NVT followed by NPT equilibration?
> > >
> > > 2. I've read that when using CHARMM36 ff in gromacs is better to switch
> > the
> > > following parameters
> > >  constraints = h-bonds
> > > cutoff-scheme = Verlet
> > > vdwtype = cutoff
> > > vdw-modifier = force-switch
> > > rlist = 1.2
> > > rvdw = 1.2
> > > rvdw-switch = 1.0
> > > coulombtype = PME
> > > rcoulomb = 1.2
> > > DispCorr = no
> > >
> > > I'm using the original mdout.mdp files produces by gromacs.Are those
> > > parameters optimal for a membrane-protein system or just for the
> lipids?
> > >
> > > Thank you all for your help.
> > > Olga
> > > --
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> >
> >
> > --
> > Shreyas Sanjay Kaptan
> > --
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-- 
Shreyas Sanjay Kaptan