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

Olga Press pressol at post.bgu.ac.il
Sun Jun 17 13:25:28 CEST 2018

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

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.

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