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

[Olga Press]

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