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

[Justin Lemkul]

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
>

-- 
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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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