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

[Alex]

What happened after 10 ns? In any case, reasonable equilibration is quite
important in these simulations to ensure lipid integrity and also avoid
protein distortions in production. Whether the structure you got after 10
ns is any good, i guess noone would know, so i'd just try to follow the
protocol for membrane equilibration.

Alex

On Jun 18, 2018 3:33 AM, "Olga Press" <pressol at post.bgu.ac.il> wrote:

Alex thank you for your advice.
I have a problem with the pre-equilibration of the membrane
before embedding the protein into it.
I've used charm-gui membrane builder website and followed the README file
at it is, including the length of the MD production and continued the
protocol as you mentioned. The problem is that at the time I've started the
simulation I produced only 10ns equilibration of the membrane.  When I've
checked the pressure it didn't reach the 1bar, and I continued the protocol
by performing log NPT equilibration (200ns)  of the entire system
(protein+membrane).
So, my question is should I start from the beginning or should I continue?
Thank you,
Olga


2018-06-18 12:02 GMT+03:00 Alex <nedomacho at gmail.com>:

> in point #1, 'it' refers to the protein. ;)
>
>
>
> On 6/18/2018 3:00 AM, Alex wrote:
>
>> 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.
>>
>> Alex
>>
>>
>> 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.
>>>
>>>
>>> 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
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>>>>>
>>>> --
>>>> Shreyas Sanjay Kaptan
>>>> --
>>>> Gromacs Users mailing list
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