[gmx-users] membrane-protein system by using charmm36 ff
nedomacho at gmail.com
Mon Jun 18 11:00:52 CEST 2018
I haven't done lipid+protein simulations in a while, but your NVT
equilibration appears to be a bit strange, because equilibration under
pressure is very important for the lipid.
Here is my general suggestion -- it may be too careful, but this is from
some experience with very poorly behaving porins:
1. Embed protein into a pre-equilibrated (semiisotropic NPT) membrane
and restrain it.
2. Run NPT equilibration of the system in multiple steps (say, a few ns
each), gradually reducing protein restraint.
3. NPT or NVT production.
The choices for thermostats/barostats for all equilibration and
production runs should be appropriate.
On 6/18/2018 2:50 AM, Olga Press 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.
> 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan <shreyaskaptan at gmail.com>:
>> 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
>>> 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
>>> 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
>>> 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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>> Shreyas Sanjay Kaptan
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