[gmx-users] Re: problem during Energy minimization

[Parul tew]

gmx-users at gromacs.org

Dear Gmx users,

I am working on a transmembrane protein and my system contains protein, DPPC
bilayer, water (spc) and ions. After preparing my system for simulation I
have successfully performed the energy minimization, I am facing a problem
at the nvt equilibration phase of 100ps, the lipid molecules enter the voids
in the solvent leaving the protein naked. I have already used position
restraint at the inflate.gro steps, now I have read that I can use the
option to freeze the groups which I can do at the z axis to avoid the lipid
headgroups to enter the void of the solvent.  The manual suggests starting
with freezing in a constant volume simulation and afterwards using position
restraints in conjunction with constant pressure.

Now, Is it feasible if I freeze the lipids in z-axis for the whole course of
simulation or should I do it only during the equilibration phase?

Is there any alternative which I can use during simulation to avoid this?

My nvt.mdp is:

-----------------------------------------------------------

title                         = NVT equilibration for B3-DPPC

define                     = -DPOSRES         ; position restrain the
protein

; Run parameters

integrator               = md                       ; leap-frog integrator

nsteps                    = 50000                   ; 2 * 50000 = 100 ps

dt                                = 0.002                                ; 2
fs

; Output control

nstxout                   = 100                       ; save coordinates
every 0.2 ps

nstvout                  = 100                       ; save velocities every
0.2 ps

nstenergy              = 100                       ; save energies every 0.2
ps

nstlog                     = 100                       ; update log file
every 0.2 ps

; Bond parameters

continuation         = no                            ; first dynamics run

constraint_algorithm = lincs              ; holonomic constraints

constraints            = all-bonds                    ; all bonds (even
heavy atom-H bonds) constrained

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

rlist                         = 1.2                        ; short-range
neighborlist cutoff (in nm)

rcoulomb               = 1.2                        ; short-range
electrostatic cutoff (in nm)

rvdw                       = 1.2                        ; short-range van
der Waals cutoff (in nm)

; Electrostatics

coulombtype         = PME                    ; Particle Mesh Ewald for
long-range electrostatics

pme_order             = 4                               ; cubic
interpolation

fourierspacing      = 0.16                      ; grid spacing for FFT

; Temperature coupling is on

tcoupl                     = V-rescale                        ; modified
Berendsen thermostat

tc-grps                   = Protein DPPC SOL_CL-   ; three coupling groups -
more accurate

tau_t                       = 0.1        0.1           0.1
; time constant, in ps

ref_t                        = 323       323          323                  ;
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                = EnerPres             ; account for cut-off vdW
scheme

; Velocity generation

gen_vel                  = yes                      ; assign velocities from
Maxwell distribution

gen_temp              = 323                       ; 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                                = 1

comm-mode           = Linear

comm-grps            = Protein_DPPC SOL_CL-

----------------------------------------------------------------------------------------
thanks,
Parul Tewatia
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