[gmx-users] NVT equilibration of protein on membrane surface
Olga Press
pressol at post.bgu.ac.il
Tue Oct 29 10:04:19 CET 2019
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).
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
> >>>>
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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
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
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> >> send a mail to gmx-users-request at gromacs.org.
> >
> >
>
> --
> ==================================================
>
> 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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>
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--
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel
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