[gmx-users] NVT equilibration of protein on membrane surface
Justin Lemkul
jalemkul at vt.edu
Mon Oct 28 13:59:07 CET 2019
On 10/28/19 3:27 AM, Olga Press wrote:
> Prof. Justin thanks so much for the explanation.
> Why this phenomenon was not observed during the NVT equilibration when I
> run a simulation of embedded protein?
A protein alone in water is surrounded by an isotropic medium that does
not exhibit the same differences (anisotropy) in forces that are
inherent to membranes.
> Do two equilibrations of NPT assemble, first with position restraint on the
> protein (50ns) and second without restains (about 200ns) will be sufficient
> to fix the problem?
You should be able to resolve the bubble faster than that.
-Justin
> Thanks a lot
> Olga
>
> בתאריך יום א׳, 27 באוק׳ 2019 ב-20:45 מאת Justin Lemkul <jalemkul at vt.edu
> >:
>
>>
>> On 10/27/19 1:20 PM, Olga Press wrote:
>>> Prof. Justin thank you for replay.
>>> The leaflets are not simply separating, the membrane is deformed and
>>> resembles a "chromosome".
>>> The image is in the following URL:
>>>
>> https://spaces.hightail.com/space/8l6z0Tncyv/files/fi-f3882907-6f37-4230-8c12-40b1f7b1ef22/fv-41ef812d-a030-412f-890f-677af406ebe6/on%20DOPC.JPG
>>> The protein is on the DOPC surface, that's why I'm not sure about the
>>> setting of the .mdp file. I used the same .mdp settings for
>>> the membrae-protein system, where the protein is embedded in a membrane.
>>> I would be very grateful if you can help me with that.
>> What you're observing is exactly what I was talking about. It's a bubble
>> in the membrane, leading to the separation of the leaflets. This comes
>> from in adequate water to fill the volume of the unit cell; the waters
>> (which diffuse much faster than the lipids) rush to fill void space and
>> equilibrate their density, but since the ensemble is NVT, the box cannot
>> change size, leaving voids where the waters were. The lipids expand to
>> fill the voids (the polar head groups are drawn to the waters more
>> strongly than the lipid tails are held together) and you get a bubble.
>> Continuing with a sufficiently long NPT relaxation will fix this.
>>
>> -Justin
>>
>>> Best regards,
>>> Olga
>>>
>>>
>>>
>>> בתאריך יום א׳, 27 באוק׳ 2019 ב-18:04 מאת Justin Lemkul <
>> jalemkul at vt.edu
>>> >:
>>>
>>>> On 10/27/19 11:10 AM, Olga Press wrote:
>>>>> Dear Gromacs users,
>>>>> I run 10ns NVT equilibration with position restains (on the protein)
>> for
>>>> a
>>>>> system in which the protein is on the membrane surface.
>>>>> I used the following .mdp file
>>>>>
>>>>> title = NVT equilibration for p1-DOPC
>>>>> define = -DPOSRES ; position restrain the protein
>>>>> ; Run parameters
>>>>> integrator = md ; leap-frog integrator
>>>>> nsteps = 5000000 ; 0.002ps * 5000000 = 10000
>>>> ps=10ns
>>>>> dt = 0.002 ; 2 fs
>>>>>
>>>>> ; OUTPUT CONTROL OPTIONS
>>>>> ; Output frequency for coords (x), velocities (v) and forces (f)
>>>>> nstxout = 0
>>>>> nstvout = 0
>>>>> nstfout = 0
>>>>> ; Output frequency for energies to log file and energy file
>>>>> nstlog = 10000
>>>>> nstcalcenergy = 100
>>>>> nstenergy = 1000
>>>>> ; Output frequency and precision for .xtc file
>>>>> nstxout-compressed = 10000
>>>>> compressed-x-precision = 1000
>>>>> ; This selects the subset of atoms for the compressed
>>>>> ; trajectory file. You can select multiple groups. By
>>>>> ; default, all atoms will be written.
>>>>> compressed-x-grps =
>>>>> ; Selection of energy groups
>>>>> energygrps =
>>>>> ; Bond parameters
>>>>> continuation = no ; first dynamics run
>>>>> constraint_algorithm = lincs ; holonomic constraints
>>>>> constraints = h-bonds ; H bonds constrained
>> fit
>>>>> to charmm36 ff
>>>>> lincs_iter = 1 ; accuracy of LINCS
>>>>> lincs_order = 4 ; also related to accuracy
>>>>> ; Neighborsearching
>>>>> ns_type = grid ; search neighboring grid cels
>>>>> nstlist = 5 ; 10 fs
>>>>> cutoff-scheme = Verlet
>>>>> vdwtype = cutoff
>>>>> vdw-modifier = force-switch ; same as vfswitch
>>>>> rvdw-switch = 1.0
>>>>> rlist = 1.2 ; short-range neighborlist cutoff (in
>> nm)
>>>>> rcoulomb = 1.2 ; short-range electrostatic cutoff (in
>>>> nm)
>>>>> ; Electrostatics
>>>>> coulombtype = PME ; Particle Mesh Ewald for long-range
>>>>> electrostatics
>>>>> pme_order = 4 ; cubic interpolation
>>>>> fourierspacing = 0.12 ; grid spacing for FFT
>>>>> ; Temperature coupling is on
>>>>> tcoupl = V-rescale ; modified Berendsen
>>>> thermostat
>>>>> *tc-grps = Protein DOPC SOL_SOD_CLA* ; three coupling
>>>> groups -
>>>>> more accurate
>>>>> tau_t = 0.1 0.1 0.1 ; time constant, in ps
>>>>> ref_t = 310.15 310.15 310.15 ; reference
>> temperature,
>>>>> one for each group, in K
>>>>> ; Pressure coupling is off
>>>>> pcoupl = no ; no pressure coupling in NVT
>>>>> ; Periodic boundary conditions
>>>>> pbc = xyz ; 3-D PBC
>>>>> ; Dispersion correction
>>>>> DispCorr = no ; Do not apply dispertion correction for
>> bilayers
>>>>> by using charmm36 ff
>>>>> ; Velocity generation
>>>>> gen_vel = yes ; assign velocities from Maxwell
>>>>> distribution
>>>>> gen_temp = 310.15 ; temperature for Maxwell
>>>>> distribution
>>>>> gen_seed = -1 ; generate a random seed
>>>>> ; COM motion removal
>>>>> ; These options remove motion of the protein/bilayer relative to the
>>>>> solvent/ions
>>>>> nstcomm = 100
>>>>> comm-mode = Linear
>>>>> *comm-grps = Protein_DOPC SOL_SOD_CLA*
>>>>>
>>>>> However, the membrane seems to be breaking apart, the image of the
>> system
>>>>> is attached to the mail.
>>>> The mailing list does not accept attachments. If you wish to share a
>>>> file or an image, upload it to a file-sharing service and provide a URL.
>>>> If the leaflets are simply separating, this is normal during NVT and
>>>> will resolve when running NPT.
>>>>
>>>> -Justin
>>>>
>>>>> I think that it is the issue of the center-of-mass motion removal, but
>>>> I'm
>>>>> not sure and would be very grateful for any suggestions.
>>>>> Best regards,
>>>>> Olga
>>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Office: 301 Fralin Hall
>>>> Lab: 303 Engel Hall
>>>>
>>>> Virginia Tech Department of Biochemistry
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>>>> Gromacs Users mailing list
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at
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>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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