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

[Olga Press]

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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