[gmx-users] NVT equilibration of protein on membrane surface

Justin Lemkul jalemkul at vt.edu
Tue Oct 29 13:45:29 CET 2019 


On 10/29/19 4:44 AM, Olga Press wrote:
> Prof. Lemkul thank you for your replay.
>   I was inaccurate with my question, what I mean is: why does the "bubble"
> phenomenon does not occur during the NVT equilibration in a system where
> the protein is  embedded inside a *membrane*? (I observed this phenomenon
> only when the protein is on the membrane surface).

I don't know anything about how you constructed the system, but with the 
protein in solution, that creates more void space around the protein 
that has to be filled by the water. When the protein is embedded, there 
is less of an impact.

-Justin

> Thank you so much for your help.
> Olga
>
>
> ‫בתאריך יום ב׳, 28 באוק׳ 2019 ב-14:59 מאת ‪Justin Lemkul‬‏ <‪jalemkul at vt.edu
> ‬‏>:‬
>
>>
>> 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
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * 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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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>>>> posting!
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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
>>
>> * Please search the archive at
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>> posting!
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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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