[gmx-users] problem with lipid membrane

[Justin A. Lemkul]

Parul tew wrote:
> Thanks for the reply Justin,
>  
> 
>      > In theory, that should work.  Please post the entirety of your
>     .mdp file.
> 
>     Have you done any prior equilibration, or have you moved straight into
>     annealing?  I would suggest a restrained NVT before applying NPT or
>     annealing
>     when using the restraints.
> 
> Yes I did the restrained NVT before but the same problem came, 
> morover there was a hole in the upper part of the system with the SOL 
> molecules displaced. So then I tried to run the annealing but in this 

I'm having trouble visualizing this.  Is the gap between the lipids and water 
molecules, or somewhere else?

> case the SOL molecules were intact but similar problem came with the 
> lipid membrane. though, just to check then I tried to equilibration with 
> restrained NVT where I restrained the movement of the lipid in all the 
> x, y, z axis the problem did not occur.
> 

I suppose this will work, although in principle it should not be necessary. 
Recall, though, that restraints are only a biasing potential and do not prevent 
movement, they simply disfavor it.  If a system is wildly far away from 
equilibrium, typical restraints can be overcome to some extent.

-Justin

>  
> 
> Here is my mdp file
> 
>  --------------------------------------------------------------------------
> 
> title       = NVT equilibration for B3-DPPC
> 
> define            = -DPOSRES -DPOSRES_LIPID     ; position restrain the 
> protein and lipid
> 
>  
> 
> ; 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-
> 
> --------------------------------------------------------------------------
> 
> This is the topology file:
> 
>  --------------------------------------------------------------------------
> 
> ;Include DPPC chain topology
> 
> #include "dppc.itp"
> 
> #ifdef POSRES_LIPID
> 
> ; Position restraint for each lipid
> 
> #include "lipid_posre.itp"
> 
> #endif
> 
> 　
> 
> ; Include water topology
> 
> #include "spc.itp"
> 
> #ifdef POSRES_WATER
> 
> ; Position restraint for each water oxygen
> 
> [ position_restraints ]
> 
> ; i funct fcx fcy fcz
> 
> 1 1 1000 1000 1000
> 
> #endif
> 
> ; Include generic topology for ions
> 
> #include "ions.itp"
> 
> 　
> 
> [ system ]
> 
> ; Name
> 
> protein
> 
> 128-Lipid DPPC Bilayer
> 
> [ molecules ]
> 
> ; Compound #mols
> 
> Protein_A 1
> 
> DPPC 121
> 
> 　
> 
> SOL 9867
> 
> CL- 14
> 
> --------------------------------------------------------------------------
> 
> thanks
> 
> Parul Tewatia
> 
>  
> 

-- 
========================================

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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