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

[Olga Press]

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