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

Shreyas Kaptan shreyaskaptan at gmail.com
Sun Jun 17 14:34:28 CEST 2018


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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

Shreyas Sanjay Kaptan

More information about the gromacs.org_gmx-users mailing list