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

Olga Press pressol at post.bgu.ac.il
Mon Oct 28 08:47:24 CET 2019


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?
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?
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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> >
>
> --
> ==================================================
>
> 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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-- 
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel


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