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

[Alex]

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
>>>> -- 
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>>>
>>> -- 
>>> Shreyas Sanjay Kaptan
>>> -- 
>>> Gromacs Users mailing list
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>