[gmx-users] problem of lipid molecules entering voids of solvent during equilibration

[Justin A. Lemkul]

Parul tew wrote:
> 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?
> 

It would make no sense to artificially immobilize the lipids during data 
collection.  Your simulation would be inherently non-equilibrium.

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

It is easier to simply use position restraints during equilibration.  That would 
be my suggestion.

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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